The outputs are found here:

/oak/stanford/groups/akundaje/projects/atlas/dnase_processed/aggregate_outputs/

The map of pipeline hash to ENCODE ID is here:

/oak/stanford/groups/akundaje/projects/atlas/dnase_processed/processed_all.txt

• bowtie2_bams.txt -- unfiltered bam files
• fc_bigwig -- fold change bigwigs
• pval_bigwig -- pval bigwigs
• merged.nodup.tagAligns.txt -- filtered tagAligns
• overlap.optimal.narrowPeak -- optimal overlap narrowPeaks
• idr.optimal.narrowPeak -- idr narrowPeaks
• qc.html.txt -- qc html files
• qc.json.txt -- qc json files

• ambiguous.optimal.narrowPeak -- Overlap peaks minus IDR peaks + 3 blacklists

• bamCoverage.aligned.bw -- produced with command

  bamCoverage -p16 -v --samFlagExclude 4 -b $cur_bam -o $cur_bam.bw
  

• bpnet.5pcounts.minus.txt

• bpnet.5pcounts.plus.txt

• bpnet.5pcounts.unstranded.txt -- bpnet count tracks are produced with this script:

  source activate encode-atac-seq-pipeline
  #non-stranded (can be PE or SE) 
  bamCoverage -p16 -v --binSize 1 --samFlagExclude 780 --Offset 1 1 --minMappingQuality 30 -b $cur_bam -o $cur_bam.bpnet.unstranded.bw
  #forward strand -- assumes SE data
  bamCoverage -p16 -v --binSize 1 --samFlagExclude 796 --Offset 1 1 --minMappingQuality 30 -b $cur_bam -o $cur_bam.bpnet.plus.bw
  #reverse strand -- assumes SE data
  bamCoverage -p16 -v --binSize 1 --samFlagExclude 780 --samFlagInclude 16 --Offset 1 1 --minMappingQuality 30 -b $cur_bam -o $cur_bam.bpnet.minus.bw
  

• nodup.5counts.plus.txt

• nodup.5pcounts.minus.txt -- 5' counts from the tagAlign -- note these differ from the bpnet counts in that duplicates have been removed and other filters have been applied. produced with command

  chromsizes=hg38.chrom.sizes
  #plus strand
  genomeCoverageBed -strand + -5 -bg -i $tagAlign -g $chromsizes > $tagAlign.tmp 
  sort -k1,1 -k2,2n  $tagAlign.tmp >  $tagAlign.counts.plus.bg
  rm $tagAlign.tmp 
  bedGraphToBigWig $tagAlign.counts.plus.bg $chromsizes $tagAlign.counts.plus.bw
  
  #minus strand 
  genomeCoverageBed -strand - -5 -bg -i $tagAlign -g $chromsizes > $tagAlign.tmp
  sort -k1,1 -k2,2n $tagAlign.tmp >  $tagAlign.counts.minus.bg
  rm $tagAlign.tmp 
  bedGraphToBigWig $tagAlign.counts.minnus.bg $chromsizes $tagAlign.counts.minus.bw
  

• mitra/fc.bigwig.mitra
• mitra/pval.bigwig.mitra
• mitra/idr.optimal.narrowPeak.mitra
• mitra/overlap.optimal.narrowPeak.mitra
• mitra/qc.html.mitra.txt