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.
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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 | 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 | * .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) |
| 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 |