Index of /kundaje/marinovg/oak/Skin_differentiation_project/2017-05-12-RNA-seq-remap

[ICO]NameLast modifiedSizeDescription

[PARENTDIR]Parent Directory  -  
[TXT]BAMtoFASTQ.sh2017-06-13 20:40 4.2K 
[TXT]GTFstats.sh2017-06-12 17:10 3.9K 
[DIR]MAJIQ/2017-05-22 21:47 -  
[TXT]MarkDuplicates-PAS-seq-2x100mers.sh2017-06-10 09:33 13K 
[TXT]MarkDuplicates.sh2017-05-30 13:17 12K 
[TXT]PAS-seq-clusters-V2-reannotation-dedup-removeAAA-V2.sh2017-06-24 00:24 15K 
[TXT]PAS-seq-clusters-dedup-removeAAA.sh2017-06-12 00:22 13K 
[TXT]PAS-seq-clusters-dedup.sh2017-06-11 23:48 10K 
[TXT]PAS-seq-clusters-reannotation-dedup-removeAAA.sh2017-06-12 22:15 14K 
[TXT]PAS-seq-clusters-reannotation-dedup.sh2017-06-12 22:14 12K 
[TXT]PAS-seq-clusters-reannotation-removeAAA.sh2017-06-12 22:15 14K 
[TXT]PAS-seq-clusters-reannotation.sh2017-06-12 22:14 12K 
[TXT]PAS-seq-clusters-removeAAA.sh2017-06-12 00:22 13K 
[TXT]PAS-seq-clusters.sh2017-06-11 23:48 10K 
[DIR]PAS-seq-gencode_v19/2017-06-25 05:44 -  
[DIR]PAS-seq-reannotation-V1/2017-06-25 05:43 -  
[TXT]RAMPAGE-clusters-V2-reannotation-dedup.sh2017-06-23 23:00 12K 
[TXT]RAMPAGE-clusters-dedup.sh2017-05-30 13:18 10K 
[TXT]RAMPAGE-clusters-reannotation-dedup.sh2017-06-12 22:14 12K 
[TXT]RAMPAGE-clusters-reannotation.sh2017-06-12 22:14 11K 
[TXT]RAMPAGE-clusters.sh2017-05-30 13:17 9.7K 
[DIR]RAMPAGE-gencode_v19/2017-06-25 05:44 -  
[DIR]RAMPAGE-reannotation-V1/2017-06-25 05:45 -  
[TXT]RSEM-PAS-seq-updated-annotation-STAR.sh2017-06-15 03:27 21K 
[TXT]RSEM-PAS-seq-updated-annotation-bowtie.sh2017-06-15 03:37 20K 
[TXT]RSEM-PAS-seq-updated-annotation-bowtie2.sh2017-06-15 03:51 20K 
[TXT]RSEM-PolyA-updated-annotation-STAR.sh2017-06-15 03:27 4.7K 
[TXT]RSEM-PolyA-updated-annotation-bowtie.sh2017-06-15 03:37 4.5K 
[TXT]RSEM-PolyA-updated-annotation-bowtie2.sh2017-06-15 03:51 4.4K 
[TXT]RSEM-RAMPAGE-PAS-2x100mers.sh2017-06-10 09:42 8.5K 
[TXT]RSEM-RAMPAGE-PAS.sh2017-05-31 20:41 17K 
[TXT]RSEM-RAMPAGE-updated-annotation-STAR.sh2017-06-15 03:27 20K 
[TXT]RSEM-RAMPAGE-updated-annotation-bowtie.sh2017-06-15 03:37 19K 
[TXT]RSEM-RAMPAGE-updated-annotation-bowtie2.sh2017-06-15 03:50 19K 
[TXT]RSEM-Total-updated-annotation-STAR.sh2017-06-15 03:28 4.7K 
[TXT]RSEM-Total-updated-annotation-bowtie.sh2017-06-15 03:37 4.5K 
[TXT]RSEM-Total-updated-annotation-bowtie2.sh2017-06-15 03:51 4.5K 
[TXT]RSEM-rerun-half_of_reads-updated-annotation-bowtie2.sh2017-06-22 07:19 786  
[TXT]RSEM-rerun-updated-annotation-bowtie2.sh2017-06-22 06:02 744  
[TXT]RSEM.sh2017-05-14 05:52 3.4K 
[TXT]SAMstats-PAS-2x100mers.sh2017-06-09 08:10 8.6K 
[   ]SAMstats-PAS-dedup.files2017-06-11 14:30 1.5K 
[   ]SAMstats-PAS-dedup.table2017-06-11 14:31 1.6K 
[   ]SAMstats-PAS.files2017-06-11 14:30 1.3K 
[   ]SAMstats-PAS.table2017-06-11 14:31 1.6K 
[   ]SAMstats-RAMPAGE-dedup.files2017-06-12 01:10 2.6K 
[TXT]SAMstats-dedup-PAS-seq-2x100mers.sh2017-06-09 08:15 8.9K 
[TXT]SAMstats-dedup.sh2017-05-30 13:18 8.9K 
[TXT]SAMstats-rerun.sh2017-05-28 00:09 680  
[   ]SAMstats.files2017-05-29 11:32 5.2K 
[TXT]SAMstats.sh2017-05-23 23:04 17K 
[   ]SAMstats.table2017-06-01 08:39 5.8K 
[DIR]SAMstats/2017-06-12 01:10 -  
[   ]SJ.out.RNA-seq-PolyA.clusters.min30counts.table2017-05-30 16:56 19M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.all.d0-vs-d3.filtered.table2017-05-30 19:27 11M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.all.d0-vs-d3.table2017-05-30 15:29 15M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.all.d0-vs-d6.filtered.table2017-05-30 19:27 12M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.all.d0-vs-d6.table2017-05-30 15:34 15M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.all.d3-vs-d6.filtered.table2017-05-30 19:27 12M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.all.d3-vs-d6.table2017-05-30 15:36 15M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.d0-vs-d3.table2017-05-30 14:59 11M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.d0-vs-d6.table2017-05-30 14:59 13M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.d3-vs-d6.table2017-05-30 14:59 13M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min50counts.table2017-05-30 13:43 17M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min75counts.all.table2017-05-30 18:18 15M 
[   ]SJ.out.RNA-seq-PolyA.clusters.min100counts.table2017-05-30 17:50 14M 
[   ]SJ.out.RNA-seq-PolyA.d0-vs-d3.files2017-05-30 14:57 276  
[   ]SJ.out.RNA-seq-PolyA.d0-vs-d6.files2017-05-30 14:57 276  
[   ]SJ.out.RNA-seq-PolyA.d3-vs-d6.files2017-05-30 14:57 276  
[   ]SJ.out.RNA-seq-PolyA.files2017-05-30 12:29 414  
[TXT]STAR-PAS-2x100mers.sh2017-06-09 08:07 27K 
[TXT]STAR-PAS.sh2017-05-23 20:31 24K 
[TXT]STAR-RAMPAGE-2.sh2017-05-23 19:56 7.8K 
[TXT]STAR-RAMPAGE-rerun.sh2017-05-22 23:57 3.9K 
[TXT]STAR-RAMPAGE.sh2017-05-20 22:24 18K 
[TXT]STAR.sh2017-05-14 00:36 10K 
[TXT]bedRPKMfromBAM-partition-PAS-seq-2x100mers.sh2017-06-09 17:15 19K 
[TXT]bedRPKMfromBAM-partition-dedup.sh2017-06-09 17:13 9.4K 
[TXT]bedRPKMfromBAM-partition-rerun.sh2017-06-12 11:48 742  
[TXT]bedRPKMfromBAM-partition.sh2017-06-03 18:12 23K 
[TXT]count_reads_mapped_to_transcriptome-PAS-2x100mers.sh2017-06-09 08:11 8.6K 
[TXT]count_reads_mapped_to_transcriptome.sh2017-05-28 00:09 21K 
[   ]coverage-PAS-dedup.files2017-06-11 14:26 1.6K 
[   ]coverage-PAS-dedup.table2017-06-11 14:27 38K 
[TXT]coverage-PAS-seq-2x100mers.sh2017-06-09 17:19 17K 
[   ]coverage-PAS.files2017-06-11 14:26 1.4K 
[   ]coverage-PAS.table2017-06-11 14:27 38K 
[   ]coverage.files2017-06-09 08:00 8.9K 
[TXT]coverage.sh2017-06-03 17:12 21K 
[   ]coverage.table2017-06-09 08:01 94K 
[DIR]coverage/2017-06-11 14:27 -  
[   ]gencode.v19.annotation.TSS-CDS-UTR2017-06-03 17:55 8.0M 
[   ]gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition2017-06-03 18:50 17M 
[   ]gencode.v19.annotation.gtf.stats-vs-PolyA+Total-with_annotation.merge.renamed-outersect12017-06-12 19:50 439  
[   ]gencode.v19.annotation.gtf.stats.individual_transcript_stats2017-06-12 19:53 17M 
[   ]gencode.v19.annotation.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 19:49 1.1M 
[   ]gencode.v19.annotation.gtf.stats.intron_stats2017-06-12 19:54 47M 
[   ]gencode.v19.annotation.partition.RPM.files2017-06-03 18:13 7.6K 
[DIR]gencode.v19.annotation.partition.RPM/2017-06-23 22:19 -  
[TXT]gzip-wiggle.sh2017-05-22 21:43 26K 
[TXT]gzip-wiggle2.sh2017-06-10 09:36 17K 
[TXT]gzip.sh2017-05-22 21:37 9.9K 
[DIR]leafCutter/2017-06-12 02:57 -  
[TXT]make5wiggle.sh2017-05-25 07:15 37K 
[TXT]makewig-dedup-PAS-seq-2x100mers.sh2017-06-09 17:18 55K 
[TXT]makewig-dedup.sh2017-05-31 10:24 46K 
[TXT]makewig-rerun.sh2017-05-25 07:15 4.4K 
[TXT]makewiggle-PAS-2x100mers.sh2017-06-09 08:10 53K 
[TXT]makewiggle-RAMPAGE-rerun.sh2017-06-12 01:44 23K 
[TXT]makewiggle.sh2017-06-03 17:09 87K 
[DIR]old_files/2017-05-30 08:24 -  
[DIR]raw_read_counts/2017-06-12 01:06 -  
[TXT]raw_read_counts_count.sh2017-06-12 01:04 11K 
[TXT]rsem-prepare-reference.sh2017-06-13 21:27 536  
[   ]sam_reads_in_genes-PAS-dedup.files2017-06-11 14:28 1.8K 
[   ]sam_reads_in_genes-PAS-dedup.table2017-06-11 14:29 1.4K 
[TXT]sam_reads_in_genes-PAS-seq-2x100mers.sh2017-06-09 17:16 21K 
[   ]sam_reads_in_genes-PAS.files2017-06-11 14:28 1.7K 
[   ]sam_reads_in_genes-PAS.table2017-06-11 14:29 1.3K 
[   ]sam_reads_in_genes.files2017-06-03 17:06 6.1K 
[TXT]sam_reads_in_genes.sh2017-06-06 19:47 25K 
[   ]sam_reads_in_genes.table2017-06-07 17:03 5.2K 
[DIR]sam_reads_in_genes/2017-06-11 14:29 -  
[TXT]sampleFastqN-count-lines.sh2017-06-23 08:10 697  
[TXT]sampleFastqN.sh2017-06-22 07:17 718  
[TXT]samtools-index-1.sh2017-05-22 21:52 1.2K 
[TXT]samtools-index-2.sh2017-05-23 23:00 4.8K 
[TXT]samtools-index-PAS-seq.sh2017-06-09 17:38 4.0K 
[TXT]samtools-index-dedup-PAS-seq-2x100mers.sh2017-06-09 08:14 4.2K 
[TXT]samtools-index-dedup.sh2017-05-30 13:18 4.2K 
[TXT]stringtie-PAS-seq-2x100mers.sh2017-06-09 08:12 20K 
[DIR]stringtie-files/2017-06-25 05:52 -  
[TXT]stringtie-merge.sh2017-06-12 15:25 3.9K 
[TXT]stringtie-rerun.sh2017-05-30 07:54 792  
[TXT]stringtie.sh2017-05-30 13:12 30K 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.files2017-06-12 01:17 2.5K 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.gtf2017-06-12 15:37 256M 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.gtf.stats.individual_transcript_stats2017-06-12 19:54 23M 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 1.4M 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.gtf.stats.intron_stats2017-06-12 19:54 57M 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.renamed.gtf2017-06-12 19:52 193M 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats2017-06-12 19:55 24M 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 1.6M 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats.transcript-hist2017-06-12 20:43 4.7M 
[   ]stringtie1.3.3b.PAS-seq-with_annotation.merge.renamed.gtf.stats.intron_stats2017-06-12 19:55 58M 
[   ]stringtie1.3.3b.PAS-seq.files2017-06-12 01:17 2.1K 
[   ]stringtie1.3.3b.PAS-seq.merge.gtf2017-06-12 15:28 42M 
[   ]stringtie1.3.3b.PAS-seq.merge.gtf.stats.individual_transcript_stats2017-06-12 19:52 9.9M 
[   ]stringtie1.3.3b.PAS-seq.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 1.2M 
[   ]stringtie1.3.3b.PAS-seq.merge.gtf.stats.intron_stats2017-06-12 19:52 9.0M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.files2017-06-12 16:53 1.2K 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.gtf2017-06-12 17:02 244M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.gtf.stats.individual_transcript_stats2017-06-12 19:55 19M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 919K 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.gtf.stats.intron_stats2017-06-12 19:55 57M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf2017-06-12 19:58 190M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats2017-06-12 19:56 20M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 1.1M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats.transcript-hist2017-06-12 20:43 4.0M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.gtf.stats.intron_stats2017-06-12 19:56 58M 
[   ]stringtie1.3.3b.PolyA+Total-with_annotation.merge.renamed.nounstranded.gtf2017-06-13 16:12 190M 
[   ]stringtie1.3.3b.PolyA+Total.files2017-06-12 16:53 1.1K 
[   ]stringtie1.3.3b.PolyA+Total.merge.gtf2017-06-12 17:00 45M 
[   ]stringtie1.3.3b.PolyA+Total.merge.gtf.stats.individual_transcript_stats2017-06-12 19:53 2.8M 
[   ]stringtie1.3.3b.PolyA+Total.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 203K 
[   ]stringtie1.3.3b.PolyA+Total.merge.gtf.stats.intron_stats2017-06-12 19:53 16M 
[   ]stringtie1.3.3b.PolyA-with_annotation.files2017-06-12 01:17 630  
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.gtf2017-06-12 15:33 235M 
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.gtf.stats.individual_transcript_stats2017-06-12 19:54 18M 
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 929K 
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.gtf.stats.intron_stats2017-06-12 19:54 55M 
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.renamed.gtf2017-06-12 19:52 180M 
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats2017-06-12 19:55 19M 
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 1.1M 
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats.transcript-hist2017-06-12 20:43 3.9M 
[   ]stringtie1.3.3b.PolyA-with_annotation.merge.renamed.gtf.stats.intron_stats2017-06-12 19:55 56M 
[   ]stringtie1.3.3b.PolyA.files2017-06-12 01:17 534  
[   ]stringtie1.3.3b.PolyA.merge.gtf2017-06-12 15:26 36M 
[   ]stringtie1.3.3b.PolyA.merge.gtf.stats.individual_transcript_stats2017-06-12 19:52 2.5M 
[   ]stringtie1.3.3b.PolyA.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 201K 
[   ]stringtie1.3.3b.PolyA.merge.gtf.stats.intron_stats2017-06-12 19:52 14M 
[   ]stringtie1.3.3b.RAMPAGE-with_annotation.files2017-06-12 01:17 2.5K 
[   ]stringtie1.3.3b.RAMPAGE-with_annotation.merge.gtf2017-06-12 15:36 253M 
[   ]stringtie1.3.3b.RAMPAGE-with_annotation.merge.gtf.stats.individual_transcript_stats2017-06-12 19:54 21M 
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[   ]stringtie1.3.3b.RAMPAGE-with_annotation.merge.renamed.gtf2017-06-12 19:52 195M 
[   ]stringtie1.3.3b.RAMPAGE-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats2017-06-12 19:55 22M 
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[   ]stringtie1.3.3b.RAMPAGE-with_annotation.merge.renamed.gtf.stats.intron_stats2017-06-12 19:55 59M 
[   ]stringtie1.3.3b.RAMPAGE.files2017-06-12 01:17 2.1K 
[   ]stringtie1.3.3b.RAMPAGE.merge.gtf2017-06-12 15:27 38M 
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[   ]stringtie1.3.3b.Total-with_annotation.files2017-06-12 01:18 648  
[   ]stringtie1.3.3b.Total-with_annotation.merge.gtf2017-06-12 15:34 235M 
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[   ]stringtie1.3.3b.Total-with_annotation.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 924K 
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[   ]stringtie1.3.3b.Total-with_annotation.merge.renamed.gtf2017-06-12 19:52 181M 
[   ]stringtie1.3.3b.Total-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats2017-06-12 19:55 19M 
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[   ]stringtie1.3.3b.Total-with_annotation.merge.renamed.gtf.stats.individual_transcript_stats.transcript-hist2017-06-12 20:43 3.9M 
[   ]stringtie1.3.3b.Total-with_annotation.merge.renamed.gtf.stats.intron_stats2017-06-12 19:55 56M 
[   ]stringtie1.3.3b.Total.files2017-06-12 01:17 552  
[   ]stringtie1.3.3b.Total.merge.gtf2017-06-12 15:27 32M 
[   ]stringtie1.3.3b.Total.merge.gtf.stats.individual_transcript_stats2017-06-12 19:52 1.9M 
[   ]stringtie1.3.3b.Total.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 165K 
[   ]stringtie1.3.3b.Total.merge.gtf.stats.intron_stats2017-06-12 19:52 13M 
[   ]stringtie1.3.3b.all-with-annotation.files2017-06-12 14:46 5.7K 
[   ]stringtie1.3.3b.all-with-annotation.merge.gtf2017-06-12 15:43 280M 
[   ]stringtie1.3.3b.all-with-annotation.merge.gtf.stats.individual_transcript_stats2017-06-12 19:54 24M 
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[   ]stringtie1.3.3b.all-with-annotation.merge.gtf.stats.intron_stats2017-06-12 19:55 63M 
[   ]stringtie1.3.3b.all-with-annotation.merge.renamed.gtf2017-06-12 19:52 219M 
[   ]stringtie1.3.3b.all-with-annotation.merge.renamed.gtf.stats.individual_transcript_stats2017-06-12 19:56 26M 
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[   ]stringtie1.3.3b.all.merge.gtf2017-06-12 15:32 69M 
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[   ]stringtie1.3.3b.all_with_ribozero-with-annotation.files2017-06-12 14:46 6.3K 
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[   ]stringtie1.3.3b.all_with_ribozero-with-annotation.merge.renamed.gtf2017-06-12 19:52 225M 
[   ]stringtie1.3.3b.all_with_ribozero-with-annotation.merge.renamed.gtf.stats.individual_transcript_stats2017-06-12 19:55 26M 
[   ]stringtie1.3.3b.all_with_ribozero-with-annotation.merge.renamed.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 1.5M 
[   ]stringtie1.3.3b.all_with_ribozero-with-annotation.merge.renamed.gtf.stats.individual_transcript_stats.transcript-hist2017-06-12 20:43 5.1M 
[   ]stringtie1.3.3b.all_with_ribozero-with-annotation.merge.renamed.gtf.stats.intron_stats2017-06-12 19:55 65M 
[   ]stringtie1.3.3b.all_with_ribozero.files2017-06-12 14:46 5.3K 
[   ]stringtie1.3.3b.all_with_ribozero.merge.gtf2017-06-12 15:30 73M 
[   ]stringtie1.3.3b.all_with_ribozero.merge.gtf.stats.individual_transcript_stats2017-06-12 19:53 8.9M 
[   ]stringtie1.3.3b.all_with_ribozero.merge.gtf.stats.individual_transcript_stats.geneID-hist2017-06-12 20:38 640K 
[   ]stringtie1.3.3b.all_with_ribozero.merge.gtf.stats.intron_stats2017-06-12 19:53 22M 
[   ]stringtie1.3.3b.gtf.files2017-06-12 01:17 1.1K 
[   ]test.bam2017-06-24 00:30 7.3M 
[   ]test.bam.bai2017-06-24 00:30 41K 
[   ]test.bed2017-05-15 07:56 153K 
[   ]test.zzz2017-06-24 00:30 129K 
[   ]z2017-06-24 18:56 12K 

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