Output specification for chip.wdlΒΆ
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.
Some summarizing QC files do not have any prefix. Find qc.json and qc.html for final QC and HTML report.
DNANexus: If you choose to usedxWDLand run pipelines on DNANexus platform, then output will be stored on the specified output directory without any subdirectories.Cromwell: OtherwiseCromwellwill store outputs for each task undercromwell-executions/[WORKFLOW_ID]/call-[TASK_NAME]/shard-[IDX]. For all tasks exceptidrandoverlap,[IDX]means a zero-based index for each replicate but for tasksidrandoverlapit 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-2should be an output directory for the pair of replicate 2 and 3.
For more details, refer to the file table section in an HTML report generated by the pipeline. Files marked as (E) are outputs to be uploaded during ENCODE accession.
| Task name | File | Description |
|---|---|---|
| merge_fastq | merge_fastqs_R?_*.fastq.gz | Merged FASTQ |
| trim_fastq | *.trim_*bp.fastq.gz | Trimmed FASTQ |
| bwa | *.bam | Raw BAM |
| bwa | *.bai | BAI for Raw BAM |
| bwa | *.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 |
| fingerprint | *.jsd.qc | DeepTools fingerprint log |
| fingerprint | *.png | DeepTools fingerprint plot |
| choose_ctl | ctl_for_rep*.tagAlign.gz | Chosen control for each IP replicate |
| 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 | MACS2 NARROWPEAK |
| macs2 | *.bfilt.narrowPeak.gz | Blacklist-filtered NARROWPEAK |
| macs2 | *.pval.signal.bigwig | p-val signal BIGWIG |
| macs2 | *.fc.signal.bigwig | fold enrichment signal BIGWIG |
| macs2 | *.frip.qc | Fraction of read (TAG-ALIGN) in peaks (NARROWPEAK) |
| spp | *.regionPeak.gz | SPP NARROWPEAK (REGIONPEAK) |
| spp | *.bfilt.narrowPeak.gz | Blacklist-filtered NARROWPEAK |
| spp | *.frip.qc | Fraction of read (TAG-ALIGN) in peaks (NARROWPEAK) |
| idr | *.*Peak.gz | IDR NARROWPEAK |
| idr | *.bfilt.*Peak.gz | Blacklist-filtered IDR NARROWPEAK |
| 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 | *.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 | conservative_peak.gz | Conservative final peak file. |
| qc_report | qc.html | Final HTML QC report |
| qc_report | qc.json | Final QC JSON |