slopBed chromsizes filter on raw MACS2 output #51
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Did you try it on data that has the bad peaks and see if this fixes it? |
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I've asked the person for the file - see #50 - I'll give it a try and let you know, though it seems pretty clear that MACS2 is outputting a peak that goes beyond the chromosome length. will keep you guys updated |
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LGTM actually and I am seeing this issue. I will try it and check that this fixes it |
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Sometimes MACS2 produces outputs (peaks and bedgraphs) that extend beyond the annotated chromosome lengths. Downstream tools (UCSC tools in particular) will complain about this. To fix, I put a slopBed in the sorting/cleaning steps of the MACS2 peak calling pipeline (going from raw MACS2 output into cleaned up files). Have run a test w/ ATAC data to make sure these don't break the pipeline, might be good to get second confirmation from one more run by someone else.