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/usr/lib/trinityrnaseq/sample_data
/usr/share/doc/trinityrnaseq-examples/changelog.Debian.gz
/usr/share/doc/trinityrnaseq-examples/changelog.gz
/usr/share/doc/trinityrnaseq-examples/copyright
/usr/share/trinityrnaseq/sample_data/Makefile
/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/Trinity.fasta.pslx
/usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/Trinity.fasta.pslx.FL_selected
/usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/Trinity.fasta.pslx.maps
/usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/Trinity.fasta.pslx.maps.summary
/usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/Trinity.fasta.pslx.stats
/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/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/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/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/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/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/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/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/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/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/__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_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_include_supertranscripts.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_no_cleanup.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_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.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
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/usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/reads.right.fq.gz
/usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/reads2.left.fq.gz
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/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/Makefile
/usr/share/trinityrnaseq/trinity_ext_sample_data/README.md
/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/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
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/usr/share/trinityrnaseq/trinity_ext_sample_data/test_DATA/Trinity.fasta.gmap/Trinity.fasta.gmap.chromosome.iit
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/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
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/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
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/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/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/Makefile
/usr/share/trinityrnaseq/trinity_ext_sample_data/test_DE_analysis/Spombe_example/Trinity_genes.TMM.EXPR.matrix
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