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GreenleafLab / NucleoATAC

nucleosome calling using ATAC-seq
MIT License
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BAM file for fragment sizes distribution plot #49

Closed krouskas closed 7 years ago

krouskas commented 7 years ago

Hi Alicia, I work with ATAC-Seq in human tissues and I would like to use NucleoATAC in order to produce a fragment size distribution (globally and around my peak calls). I would like to ask you which BAM file you use to produce this plot? I run PEx100 libraries in IlluminaHiSeq2000. Do I need to filter BAM files (remove duplicates, keep only properly-paired reads, high MAPQ) before applying NucleoATAC?

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AliciaSchep commented 7 years ago

I use filtered bam files -- removed duplicates, improper pairs, mapq >30. The pyatac sizes command should ignore improperly paired reads though, so that filtering isn't critical.