output.md

Output specification

All output filenames keep prefixes from corresponding input filenames. For example. If you have started from REP1.fastq.gz and REP2.fastq.gz then corresponding alignment log for each replicate has a filename of REP1.flagstat.qc and REP2.flagstat.qc, respectively.

Final HTML report (qc.html) and QC json (qc.json) files do not have any prefix.

1. DNAnexus: Output will be stored on the specified output directory without any subdirectories.

2. Cromwell: Cromwell will store outputs for each task under cromwell-executions/[WORKFLOW_ID]/call-[TASK_NAME]/shard-[IDX]. For all tasks except two peak calling tasks idr (irreproducible discovery rate) and overlap (naive overlapping peaks), [IDX] means a zero-based index for each replicate. For two tasks idr and overlap, [IDX] stands for a zero-based index for all possible pair of replicates. For example, you have 3 replicates and all possible combination of two replicates are [(rep1,rep2), (rep1,rep3), (rep2,rep3)]. Therefore, call-idr/shard-2 should be an output directory for the pair of replicate 2 and 3.

There can be duplicate output files on execution/ and execution/glob-*/ directories. A file on the latter (execution/glob-*/) is a symbolic link of an actual output file on the former. For Google Cloud Storage bucket (gs://) there is no execution/ directory and files on glob-*/ are actual outputs.

task	filename	description
trim_adapter	* .trim.fastq.gz	adapter-trimmed FASTQ
trim_adapter	merge_fastqs_R?_*.fastq.gz	Merged and adapter-trimmed FASTQ
bowtie2	* .bam	Raw BAM
bowtie2	* .bai	BAI for Raw BAM
bowtie2	* .align.log	Bowtie2 log for mapping
bowtie2	* .flagstat.qc	Samtools flagstat log for raw BAM
filter	* .nodup.bam	Filtered/deduped BAM
filter	* .nodup.flagstat.qc	Samtools flagstat log for filtered/deduped BAM
filter	* .dup.qc	Picard/sambamba markdup log
filter	* .pbc.qc	PBC QC log
bam2ta	* .tagAlign.gz	TAG-ALIGN generated from filtered BAM
bam2ta	* .N.tagAlign.gz	Subsampled (N reads) TAG-ALIGN generated from filtered BAM
bam2ta	* .tn5.tagAlign.gz	TN5-shifted TAG-ALIGN
spr	* .pr1.tagAlign.gz	1st pseudo-replicated TAG-ALIGN
spr	* .pr2.tagAlign.gz	2nd pseudo-replicated TAG-ALIGN
pool_ta	* .tagAlign.gz	Pooled TAG-ALIGN from all replciates
xcor	* .cc.plot.pdf	Cross-correlation plot PDF
xcor	* .cc.plot.png	Cross-correlation plot PNG
xcor	* .cc.qc	Cross-correlation analysis score log
xcor	* .cc.fraglen.txt	Estimated fragment length
macs2	* .narrowPeak.gz	NARROWPEAK
macs2	* .bfilt.narrowPeak.gz	Blacklist-filtered NARROWPEAK
macs2	* .bfilt.narrowPeak.bb	Blacklist-filtered NARROWPEAK in BigBed format
macs2	* .frip.qc	Fraction of read (TAG-ALIGN) in peaks (NARROWPEAK)
macs2_signal_track	* .pval.signal.bigwig	p-val signal BIGWIG
macs2_signal_track	* .fc.signal.bigwig	fold enrichment signal BIGWIG
count_signal_track	* .positive.bigwig	Count signal (+ strand) BIGWIG
count_signal_track	* .negative.bigwig	Count signal (- strand) BIGWIG
idr	* .*Peak.gz	IDR NARROWPEAK
idr	* .bfilt.*Peak.gz	Blacklist-filtered IDR NARROWPEAK
idr	* .bfilt.*Peak.bb	Blacklist-filtered IDR NARROWPEAK in BigBed format
idr	* .txt.png	IDR plot PNG
idr	* .txt.gz	Unthresholded IDR output
idr	* .log	IDR STDOUT log
idr	* .frip.qc	Fraction of read (TAG-ALIGN) in peaks (IDR NARROWPEAK)
overlap	* .*Peak.gz	Overlapping NARROWPEAK
overlap	* .bfilt.*Peak.gz	Blacklist-filtered overlapping NARROWPEAK
overlap	* .bfilt.*Peak.bb	Blacklist-filtered overlapping NARROWPEAK in BigBed format
overlap	* .frip.qc	Fraction of read (TAG-ALIGN) in peaks (overlapping NARROWPEAK)
reproducibility	* .reproducibility.qc	Reproducibililty QC log
reproducibility	optimal_peak.gz	Optimal final peak file
reproducibility	optimal_peak.bb	Optimal final peak file in BigBed format
reproducibility	conservative_peak.gz	Conservative final peak file
reproducibility	conservative_peak.bb	Conservative final peak file in BigBed format
qc_report	qc.html	Final HTML QC report
qc_report	qc.json	Final QC JSON