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