Tao Liu (τν)

@mengxiao According to https://github.com/liulab-dfci/MAESTRO/blob/28e2927b938242960180a82688c955bd7c427c22/MAESTRO/scATAC_Genescore.py#L233-L237 All the peaks will be classified as either the peaks in any 'gene-bodies' (=exon+promoter)', or the peaks outside of any 'gene-bodies'. If a peak_i is in...

Please find the document for MACS2 here. Should be quite the same with MACS3. I need to make a MACS3 version for this though ... https://github.com/macs3-project/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands

@bioysu When `-call-summits` is used, MACS2 will call the subsummits in the peak region, and that's why you see `sampleName_peak_3a` and `sampleName_peak_3b`. It means there are two local maxima in...

If you followed original protocol for ATAC-Seq, you should get Paired-End reads. If so, I would suggest you just use "--format BAMPE" to let MACS2 pileup the whole fragments in...

@crazyhottommy @igordot Yes. With -f BAMPE on, MACS2 read the left mate and the insertion length information from BAM file, and discard right mate. With -f BAM, MACS2 only keeps...

> Why do so many papers use --shift -100 --extsize 200 for MACS2 rather than -f BAMPE if this is not recommended for paired-end data? --shift -100 --extsize 200 will...

@yichao-cai `--keep-dup all` is recommended if the duplicated alignments have been removed in preprocessing steps with other tools. The idea is that we shall not perform the same task with...

@igordot I just enabled the 'Discussions' function for MACS on Github: https://github.com/macs3-project/MACS/discussions Hope that the informative discussions in the 'Issues' won't go away because of age :) I can summarize...

Another related issue, as I mentioned in Xi Chen's Twitter thread, is #421. As for MACS, the goal is to enable possible ways to analyze the data, so I will...

Thank you! @igordot