The file extension below are generated by RNA-seq pipeline, the \ prefix for each file is the name fed in by the manifest polyATrim.adapterTrim.fastq.out Std out for cutadapt polyATrim.adapterTrim.metrics cutadapt metrics polyATrim.adapterTrim.rmRep_fastqc.zip zip file for fastqc post-cutadapt, post, repetitive element removal polyATrim.adapterTrim.rmRep.fastq.out std out for repetitive element removal polyATrim.adapterTrim.rmRep.metrics metrics for number of repetitive elements removed polyATrim.adapterTrim.rmRep.sam sam file mapped to reference genome polyATrim.adapterTrim.rmRep.samLog.final.out STAR specific output polyATrim.adapterTrim.rmRep.samLog.out STAR Specific output polyATrim.adapterTrim.rmRep.samLog.progress.out STAR Specific output polyATrim.adapterTrim.rmRep.samLog.std.out STAR Specific output polyATrim.adapterTrim.rmRep.sam.out STAR mapping std out polyATrim.adapterTrim.rmRep.samSJ.out.tab STAR specific output polyATrim.adapterTrim.rmRep.samUnmapped.out.mate1 STAR specific output polyATrim.adapterTrim.rmRep.sorted.bai index file for intermediate processing, ignore polyATrim.adapterTrim.rmRep.sorted.bam intermediate bam file, ignore polyATrim.adapterTrim.rmRep.sorted.bam.out std out for STAR, ignore polyATrim.adapterTrim.rmRep.sorted.rg.bai index file for intermediate processing, ignore polyATrim.adapterTrim.rmRep.sorted.rg.bam final read, group assigned bam file polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai final read, group assigned bam index file polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai.out stdout for final read, group assigned bam index file polyATrim.adapterTrim.rmRep.sorted.rg.bam.out stdout for final read, group assigned bam file polyATrim.adapterTrim.rmRep.sorted.rg.count Counts of reads at in each gene, from CountTags polyATrim.adapterTrim.rmRep.sorted.rg.count.out stdout for Counts of reads at in each gene, from CountTags polyATrim.adapterTrim.rmRep.sorted.rg.editing.out editing make file out polyATrim.adapterTrim.rmRep.sorted.rg.make.out unknown ignore polyATrim.adapterTrim.rmRep.sorted.rg.miso.out miso make file out polyATrim.adapterTrim.rmRep.sorted.rg.neg.t.bg.out stdout for genomeCoverageBed, negative strand polyATrim.adapterTrim.rmRep.sorted.rg.neg.t.bw bigWig file showing read coverage along the negative strand, transposed so values are negative polyATrim.adapterTrim.rmRep.sorted.rg.neg.t.bw.out stdout for bw file generation polyATrim.adapterTrim.rmRep.sorted.rg.neg.t.norm.bg.out stdout for bg file generation polyATrim.adapterTrim.rmRep.sorted.rg.neg.t.norm.bw read depth normalized, transposed negative strand coverage bigWig file polyATrim.adapterTrim.rmRep.sorted.rg.neg.t.norm.bw.out stdout for bigwig file generation polyATrim.adapterTrim.rmRep.sorted.rg.NRF.metrics metrics for PCR duplication, for reference see: http://genome.ucsc.edu/ENCODE/qualityMetrics.html polyATrim.adapterTrim.rmRep.sorted.rg.NRF.metrics.out stdout for NRF calculations polyATrim.adapterTrim.rmRep.sorted.rg.pos.bg.out stdout for bedgraph generation polyATrim.adapterTrim.rmRep.sorted.rg.pos.bw bigWig file showing coverage along positive strand polyATrim.adapterTrim.rmRep.sorted.rg.pos.bw.out stdout for bigwig generation polyATrim.adapterTrim.rmRep.sorted.rg.pos.norm.bg.out stdout for bedgraph generation polyATrim.adapterTrim.rmRep.sorted.rg.pos.norm.bw read depth normalized, coverage on positive strand bigWig file polyATrim.adapterTrim.rmRep.sorted.rg.pos.norm.bw.out std out for read depth normalized, coverage on positive strand bigWig file polyATrim.adapterTrim.rmRep.sorted.rg.rpkm RPKMs calculated from SingleRPKM polyATrim.adapterTrim.rmRep.sorted.rg.rpkm.out std out from RPKMs calculated from SingleRPKM polyATrim.adapterTrim.rmRep.sorted.rg.splices Old Splice Results polyATrim.adapterTrim.rmRep.sorted.rg.splices.out stdout from Old Splice Results ABANDON ALL HOPE YE WHO ENTER HERE THESE FILES ARE FROM BOKYO FOR GENERATING a->i editing analysis polyATrim.adapterTrim.rmRep.sorted.rg_stage1.bcf polyATrim.adapterTrim.rmRep.sorted.rg_stage1.bcf.bci polyATrim.adapterTrim.rmRep.sorted.rg_stage1.conf polyATrim.adapterTrim.rmRep.sorted.rg_stage1.conf0.995 polyATrim.adapterTrim.rmRep.sorted.rg_stage1.conf0.995.bb polyATrim.adapterTrim.rmRep.sorted.rg_stage1.conf0.995.bed polyATrim.adapterTrim.rmRep.sorted.rg_stage1.conf0.995.csv fastq.gz.polyATrim.adapterTrim.rmRep.sorted.rg_stage1.conf0.995.no100 polyATrim.adapterTrim.rmRep.sorted.rg_stage1.conf0.995.regions polyATrim.adapterTrim.rmRep.sorted.rg_stage1.eff10 polyATrim.adapterTrim.rmRep.sorted.rg_stage1.eff5 polyATrim.adapterTrim.rmRep.sorted.rg_stage1.eff5-10 polyATrim.adapterTrim.rmRep.sorted.rg_stage1.noSNP polyATrim.adapterTrim.rmRep.sorted.rg_stage1.sorted.bam polyATrim.adapterTrim.rmRep.sorted.rg_stage1.sorted.bam.bai polyATrim.adapterTrim.rmRep.sorted.rg_stage1.var polyATrim.adapterTrim.rmRep.sorted.rg_stage1.vcf polyATrim.adapterTrim.rmRep.sorted.rg_stage2.bam polyATrim.adapterTrim.rmRep.sorted.rg_stage2.bcf polyATrim.adapterTrim.rmRep.sorted.rg_stage2.bcf.bci polyATrim.adapterTrim.rmRep.sorted.rg_stage2.conf polyATrim.adapterTrim.rmRep.sorted.rg_stage2.conf0.995 polyATrim.adapterTrim.rmRep.sorted.rg_stage2.conf0.995.bed polyATrim.adapterTrim.rmRep.sorted.rg_stage2.conf0.995.csv polyATrim.adapterTrim.rmRep.sorted.rg_stage2.conf0.995.no100 polyATrim.adapterTrim.rmRep.sorted.rg_stage2.conf0.995.regions polyATrim.adapterTrim.rmRep.sorted.rg_stage2.eff10 polyATrim.adapterTrim.rmRep.sorted.rg_stage2.eff5 polyATrim.adapterTrim.rmRep.sorted.rg_stage2.eff5-10 polyATrim.adapterTrim.rmRep.sorted.rg_stage2.noSNP polyATrim.adapterTrim.rmRep.sorted.rg_stage2.rmdup.bam polyATrim.adapterTrim.rmRep.sorted.rg_stage2.sorted.bam polyATrim.adapterTrim.rmRep.sorted.rg_stage2.sorted.bam.bai polyATrim.adapterTrim.rmRep.sorted.rg_stage2.var polyATrim.adapterTrim.rmRep.sorted.rg_stage2.vcf polyATrim.adapterTrim.rmRep.sorted.rg_stage3.bcf polyATrim.adapterTrim.rmRep.sorted.rg_stage3.bcf.bci polyATrim.adapterTrim.rmRep.sorted.rg_stage3.eff10 polyATrim.adapterTrim.rmRep.sorted.rg_stage3.eff5 polyATrim.adapterTrim.rmRep.sorted.rg_stage3.eff5-10 polyATrim.adapterTrim.rmRep.sorted.rg_stage3.noSNP polyATrim.adapterTrim.rmRep.sorted.rg_stage3.sorted.bam polyATrim.adapterTrim.rmRep.sorted.rg_stage3.sorted.bam.bai polyATrim.adapterTrim.rmRep.sorted.rg_stage3.var polyATrim.adapterTrim.rmRep.sorted.rg_stage3.vcf