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