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How to changed the --mfold or -m paramter of macs2.1?

I have been trying to call peaks for a transcription factor using the last release of macs2.1, I have used it effectively with default parameters for chromatin marks but while am trying to use it for TFs , it gives excessively low peaks with default. So as per the warning am intending to change the mfold parameter but am unable to since it throws an error. How to change the mfold parameter in macs2.1, what is the syntax for it. I want to use an mfold which is as low as 5,30 the default is 5,50. With macs1.4 I was getting 450 peaks but with macs2.1 am getting 60 peaks.

Warning
"Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model!"

So I am trying to run lowering the mfold. I am keeping the shfit size and bandwidth same. Did anyone face this problem? I am unable to change the mfold. It throws an error.

Thanks
VD

chip-seq macs2.1 macs2
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updated by Ram Ram • written by ivivek_ngs ivivek_ngs

Hello vchris_ngs!

We believe that this post does not fit the main topic of this site.

figured it out

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

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written by ivivek_ngs ivivek_ngs

2 answers

Figured it out so I would close this question, but before that if anyone has suggestion for --shift and --extsize with macs2.1 that is usually used for TF calling with MACS2.1 in case you do not want MACS2.1 to build the model, please share, Thanks

P.S: If I get some reply within a day then I would reply else would close the query, Thanks

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updated by Ram Ram • written by ivivek_ngs ivivek_ngs

If you are having trouble with model building then use --nomodel and --extsize using a value based on your expectation of the fragment size (usually via the DNA run on a gel prior to the library prep). Usually the value is about 250bp. Unless you choose a value that is very different your summit regions should be close enough to the true binding region. I usually select a 200bp region centred on each summit for motif discovery analysis, which allows some "wiggle" without introducing too much noise.

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updated by Ram Ram • written by Ian Ian

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