trinityrnaseq-examples (2.15.2+dfsg-3)
Details
Core information at a glance
- Distribution
- ubuntu
- Origin
- ubuntu-stonking
- Repository
- https://nl.archive.ubuntu.com/ubuntu
- Codename
- stonking
- Component
- universe
- Source
- trinityrnaseq
- Architecture
- amd64
- Section
- universe/science
- Priority
- optional
- Maintainer
- Ubuntu Developers <[email protected]>
Size & integrity
Byte sizes and integrity verification
- Installed size
- 449.9 kB
- Size expected
- 298.9 MB
- Size actual
- 298.9 MB
- Size match
Suggested packages
Recommended additional packages
- None
Description
RNA-Seq De novo Assembly common example and testing files
Tags
Package classification tags
None
Checksums
Hash values and integrity verification status
| Type | Actual | Match |
|---|---|---|
| MD5 | 7468090d…11d37a90 | |
| SHA-1 | e2cf58b0…33c0ab59 | |
| SHA-256 | 5e0eb7dc…2cf2bdf1 | |
| SHA-512 | be0176ba…41e9287c |
Contents
Files and directories included
. usr usr/lib usr/lib/trinityrnaseq usr/share usr/share/doc usr/share/doc/trinityrnaseq-examples usr/share/doc/trinityrnaseq-examples/changelog.Debian.gz usr/share/doc/trinityrnaseq-examples/copyright usr/share/trinityrnaseq usr/share/trinityrnaseq/sample_data usr/share/trinityrnaseq/sample_data/Makefile usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/Makefile usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/README usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/bowtie2.sam.aligned.bam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.IGV.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/ex02.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/ex2.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/ex2.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/example2.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/region2.sam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/region2.sam.adj usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/ex03.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/ex3.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/ex3.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/example3.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/region3.sam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/region3.sam.adj usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/ex04.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/ex4.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/ex4.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/example4.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/region4.sam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/region4.sam.adj usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/clean.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/clean.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/ex05.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/ex5.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/ex5.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/example5.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta.Bfly.dot usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta.gmap.bed usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta.gmap.gff usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/region5.sam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/region5.sam.adj usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/ex06.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/ex6.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/ex6.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/example6.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/region6.sam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/region6.sam.adj usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/ex07.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/ex7.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/ex7.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/example7.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/region7.sam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/region7.sam.adj usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/ex08.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/ex8.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/ex8.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/example8.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/region8.sam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/region8.sam.adj usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09 usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/ex09.refSeq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/ex9.reads.left.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/ex9.reads.right.fq usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/example9.png usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/region9.sam usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/region9.sam.adj usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/refSeqs.fa usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/refSeqs.fa.gene_trans_map usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/cleanme.pl usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/longReads.fa usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.noSeqtk.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_CuffFly.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_PasaFly.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_as_DS.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_bowtie_components.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_docker.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_full_cleanup.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_cleanup.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_para_iworm.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_salmon.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_salmon_no_cleanup.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_symlinks.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_parallel_iworm_assembly.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_piecemeal.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_trin_complete.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_bowtie2.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_my_ramdisk.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_LSF.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_SGE.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_uger.HpcGridRunner.singularity_intra.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_uger.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_wSuperReads.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__run_PE_samples_file.min_kmer_cov_3.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__run_PE_samples_file.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__run_SE_samples_file.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__run_abundance_estimation_include_antisense.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe.singleFQ.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_NO_normalization.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_docker.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_lenient_path_extension.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_singularity.intra.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_singularity.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_with_jaccard_clip.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/misc_run_tests/runMe_no_qualTrim.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fa.gz usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.left.fq.gz usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fa.gz usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.right.fq.gz usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/runMe.sh usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/samples.PE.txt usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/samples.SE.txt usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/test_FL.sh usr/share/trinityrnaseq/trinity_ext_sample_data usr/share/trinityrnaseq/trinity_ext_sample_data/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/README.md usr/share/trinityrnaseq/trinity_ext_sample_data/__regression_tests usr/share/trinityrnaseq/trinity_ext_sample_data/__regression_tests/test_GraphFromFasta usr/share/trinityrnaseq/trinity_ext_sample_data/__regression_tests/test_GraphFromFasta/both.fa.gz usr/share/trinityrnaseq/trinity_ext_sample_data/__regression_tests/test_GraphFromFasta/inchworm.K25.L25.fa.gz usr/share/trinityrnaseq/trinity_ext_sample_data/__regression_tests/test_GraphFromFasta/iworm_scaffolds.txt.gz usr/share/trinityrnaseq/trinity_ext_sample_data/__regression_tests/test_GraphFromFasta/runMe.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings/ensure_min_asm.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings/reads.ForRev_1.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings/reads.ForRev_2.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings/reads.left.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings/reads.left.stripped.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings/reads.right.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_Assembly_DiffReadFormattings/reads.right.stripped.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_ds.10k.left.fq usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_ds.10k.left.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_ds.10k.right.fq usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_ds.10k.right.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_hs.10k.left.fq usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_hs.10k.left.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_hs.10k.right.fq usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_hs.10k.right.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_log.10k.left.fq usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_log.10k.left.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_log.10k.right.fq usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_log.10k.right.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_plat.10k.left.fq usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_plat.10k.left.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_plat.10k.right.fq usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Sp_plat.10k.right.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gene_trans_map usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.chromosome usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.chromosome.iit usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.chrsubset usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.contig usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.contig.iit usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.genomebits128 usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.genomecomp usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.ref133offsets64meta usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.ref133offsets64strm usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.ref133positions usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.sachildexc usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.sachildguide1024 usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.saindex64meta usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.saindex64strm usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.salcpchilddc usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.salcpexc usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.salcpguide1024 usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.sarray usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.version usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/candidate.Trinity_trans.TMM.EXPR.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/candidate.Trinity_trans.counts.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/candidate.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/gsnap.cSorted.bam usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/gsnap.cSorted.bam.bai usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/reads.left.fa.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/reads.left.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/reads.right.fa.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/reads.right.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/reads2.left.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/reads2.right.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/salmon-quasi-trans.isoform.TMM.EXPR.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example/Trinity_trans.TMM.EXPR.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example/Trinity_trans.TPM.not_cross_norm usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example/Trinity_trans.counts.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example/notes usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example/test_PtR_PCA usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Candida_example/validate_results.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/Trinity_genes.TMM.EXPR.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/Trinity_genes.counts.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/Trinity_genes.lengths usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/Trinotate_report.xls.gene_ontology usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/trans.seq.lengths.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/validate_results.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/cleanMe.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/compare_dexseq_results.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sA_rep1_1.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sA_rep1_2.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sA_rep2_1.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sA_rep2_2.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sA_rep3_1.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sA_rep3_2.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sB_rep1_1.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sB_rep1_2.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sB_rep2_1.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sB_rep2_2.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sB_rep3_1.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/data/sB_rep3_2.fastq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/mini.Trinity_fmt.fasta usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/minigenome.fa usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/minigenome.gtf usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/plot_comparison.Rscript usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/runMe.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_DTU/test_for_cor.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50 usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/acanth.E-inputs.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/acanth.ExN50.stats usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/axolotl.by-gene.E-inputs.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/axolotl.by-transcript.E-inputs.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/axolotl.gene.ExN50.stats usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/axolotl.transcript.ExN50.stats usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/estimate_transcript_numbers_by_expression.Rmd usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/mouse.50M.ExN50.stats usr/share/trinityrnaseq/trinity_ext_sample_data/test_ExN50/more_examples/mouse50M.E-inputs.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe/Rplots.pdf usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe/__runGOseq.R usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe/diauxic_shift_induced.GOseq.depleted usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe/diauxic_shift_induced.GOseq.enriched usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe/heatshock.GOseq.depleted usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe/heatshock.GOseq.enriched usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq/Trinity.gene.lengths usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq/Trinity_genes.TMM.EXPR.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq/Trinity_genes.counts.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq/Trinotate_report.xls.gene_ontology usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq/contrasts.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq/runMe.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_analyzeDiffExprWithGOseq/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/Trinity.background usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/Trinity.seq_lengths usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/Trinotate_report.xls usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/Trinotate_report.xls.trans.gene_ontology usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/cleanme.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/ds_induced_vs_log.factors usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/hs_induced_vs_log.factors usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Spombe_runGOseqOnly/runMe.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/from_enrichnet.org usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/from_enrichnet.org/Cancer_genes_Futreal2004.ids usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/from_enrichnet.org/Parkinsons_disease_Phenopedia2011.ids usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/test_GOplot usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/test_GOplot/EC.david usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/test_GOplot/EC.genelist usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/test_GOplot/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOplot usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOplot/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOplot/data usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOplot/data/Trinity_genes.counts.matrix.log_growth_vs_heatshock.edgeR.DE_results.P0.001_C2.DE.subset usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOplot/data/Trinity_genes.counts.matrix.log_growth_vs_heatshock.edgeR.DE_results.P0.001_C2.DE.subset.GOseq.enriched usr/share/trinityrnaseq/trinity_ext_sample_data/test_GOplot/data/Trinotate_report.xls.gene_ontology usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.annot.bed.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.SE.sam.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.bam usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/SP2.chr.fa.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.illumina.bam usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/chr17.pbio.bam usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/cleanme.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/mm9chr17.annotation.bed.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/mm9chr17.fasta.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/mm9chr17.tophat.bam usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_LSF.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_PBS.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_SGE.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.SE.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_genome-guided_Trinity.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/run_Schizo_TrinityGG_jaccard_clip.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/run_chr17_GG_wLongreads.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/run_genome-guided_Trinity_use_existing_bam.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/run_small_GG_mutliScaff_test.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/top100k.Left.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/top100k.Right.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/top100k.genome.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_GenomeGuidedTrinity/transAligns.cSorted.bam usr/share/trinityrnaseq/trinity_ext_sample_data/test_Glimma usr/share/trinityrnaseq/trinity_ext_sample_data/test_Glimma/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_Glimma/my.DE_results usr/share/trinityrnaseq/trinity_ext_sample_data/test_Glimma/my.counts.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_Glimma/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization usr/share/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/cleanme.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.mult_read_sets.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.w_base_cov_stats.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_InSilicoReadNormalization/test_SE_normalization.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_Inchworm usr/share/trinityrnaseq/trinity_ext_sample_data/test_Inchworm/jellyfish.kmers.fa.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_Inchworm/runMe_MPI.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_LongReads usr/share/trinityrnaseq/trinity_ext_sample_data/test_LongReads/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_LongReads/longreads.fa usr/share/trinityrnaseq/trinity_ext_sample_data/test_LongReads/reads_1.fa usr/share/trinityrnaseq/trinity_ext_sample_data/test_LongReads/reads_2.fa usr/share/trinityrnaseq/trinity_ext_sample_data/test_PtR usr/share/trinityrnaseq/trinity_ext_sample_data/test_PtR/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/cleanMe.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_flush usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_flush/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_flush/S-Lap3.flush.fa usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_flush/st.fasta usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_flush/st.gtf.expected_result usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_flush/st.gtf.expected_result.sort usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_fstExt usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_fstExt/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_fstExt/S-Lap3.fstExt.fa usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_fstExt/st.gtf.expected_result usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_fstExt/st.gtf.expected_result.sort usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/indiv_tests/S-Lap3_fstExt/st.gtf.expected_result.sort.alt usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/mouse.10M.altsplice.trin.fa.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/runMe.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_TPM_weighted_gene_length usr/share/trinityrnaseq/trinity_ext_sample_data/test_TPM_weighted_gene_length/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_TPM_weighted_gene_length/Trinity.fasta usr/share/trinityrnaseq/trinity_ext_sample_data/test_TPM_weighted_gene_length/Trinity.fasta.gene_trans_map usr/share/trinityrnaseq/trinity_ext_sample_data/test_TPM_weighted_gene_length/Trinity.fasta.seqlens usr/share/trinityrnaseq/trinity_ext_sample_data/test_TPM_weighted_gene_length/rsem.isoform.TMM.EXPR.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_TissueSpecificityGraph usr/share/trinityrnaseq/trinity_ext_sample_data/test_TissueSpecificityGraph/DE_results.tar.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_TissueSpecificityGraph/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_TissueSpecificityGraph/transcripts.TMM.fpkm.avg_reps.matrix.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling/samples_file.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling/small_1.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling/small_2.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling/supertranscripts.fasta usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling/supertranscripts.gtf usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling/whitefly_rnaseq_1.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_VariantCalling/whitefly_rnaseq_2.fq.gz usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/cleanme.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/drosoph_denovo.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/drosoph_ref.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/mouse_denovo.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/mouse_ref.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/schizo_denovo.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/schizo_ref.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION_via_samples_file_direct usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION_via_samples_file_direct/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION_via_samples_file_direct/cleanme.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION_via_samples_file_direct/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/cleanme.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/drosoph_denovo.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/drosoph_ref.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/mouse_denovo.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/mouse_ref.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/schizo_denovo.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/schizo_ref.samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION_via_samples_file_direct usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION_via_samples_file_direct/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION_via_samples_file_direct/cleanme.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION_via_samples_file_direct/samples.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/log.out usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/pairs.Rscript usr/share/trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/plot_paired_comparisons.Rscript usr/share/trinityrnaseq/trinity_ext_sample_data/test_filter_low_expr usr/share/trinityrnaseq/trinity_ext_sample_data/test_filter_low_expr/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_filter_low_expr/kallisto-trans.TMM.EXPR.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline usr/share/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/cleanme.pl usr/share/trinityrnaseq/trinity_ext_sample_data/test_full_edgeR_pipeline/samples_n_reads_decribed.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_profiling_report usr/share/trinityrnaseq/trinity_ext_sample_data/test_profiling_report/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_profiling_report/ex1 usr/share/trinityrnaseq/trinity_ext_sample_data/test_profiling_report/ex1/collectl.dat usr/share/trinityrnaseq/trinity_ext_sample_data/test_profiling_report/ex2 usr/share/trinityrnaseq/trinity_ext_sample_data/test_profiling_report/ex2/collectl.dat usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/Makefile usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/gene_to_trans.txt usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/plot_comparison.Rscript usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/quant_files.list usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188021 usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188021/cmd_info.json usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188021/quant.sf usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188088 usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188088/cmd_info.json usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188088/quant.sf usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188288 usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188288/cmd_info.json usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188288/quant.sf usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188297 usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188297/cmd_info.json usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188297/quant.sf usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188329 usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188329/cmd_info.json usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188329/quant.sf usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188356 usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188356/cmd_info.json usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/salmon/ERR188356/quant.sf usr/share/trinityrnaseq/trinity_ext_sample_data/test_tximport/tximport_compare.Rscript usr/lib/trinityrnaseq/sample_data usr/share/trinityrnaseq/trinity_ext_sample_data/test_PtR/candidate.Trinity_trans.TMM.EXPR.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_PtR/candidate.Trinity_trans.counts.matrix usr/share/trinityrnaseq/trinity_ext_sample_data/test_PtR/candidate.samples.txt