limiting to NFR in the dev version
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Description
How could I run the analysis with NFR only? My pipeline_info/paramsXXX.json has the right range of minFragmentLength(0) and maxFragmentLength (120). But the input bam file for macs3 callpeak is not limited to NFR. Are there any parameter(s) that I missed? Here is my command:
nextflow run dev_version/atacseq -profile singularity --input ./fastq.csv --min_trimmed_reads 0 --aligner bowtie2 --keep_dups TRUE --narrow_peak TRUE --genome hg38 --read_length 150 --outdir ./outDir_
Thanks,
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Research direction
Start with dev_version/atacseq and pipeline_info/paramsXXX.json, then trace how minFragmentLength and maxFragmentLength reach the macs3 callpeak input. Reproduce the command with the supplied hg38 and Bowtie2 options and verify that the input BAM contains only the requested NFR range.
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Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100