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macs3-project / MACS

MACS -- Model-based Analysis of ChIP-Seq
https://macs3-project.github.io/MACS/
BSD 3-Clause "New" or "Revised" License
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Q: Changing MFOLD not altering output #292

Open ashleymaeconard opened 5 years ago

ashleymaeconard commented 5 years ago

Hello, I wanted to try varying the upper and lower bound for the MFOLD parameter and I do not see any changes in the results. Can you tell me why this is? I should note that I do not have a control, and I realize that in that case, macs2 infers a noise level (i.e. background) and thus generates a control.

This is my command: macs2 callpeak -t /out.sorted.bam -B -f AUTO --nomodel --SPMR --keep-dup all -g dm --trackline -n out.sorted.bam --cutoff-analysis --call-summits -p 0.01 -m 40 100 --outdir /outdir/ 2> /outdir/out.sorted.bam.log &

I tried 3 different MFOLD boundary limits: 5 50, 25 100, and 40 100, and when examining the narrowPeak and pileup.bdg files there is no difference.

Thank you! Ashley:)

taoliu commented 5 years ago

MFOLD is used to estimate the shifting model in order to predict the 'fragment length' for smoothing pileup signals, and the actual setting may or may not have an impact on the final result. If you want to tweak 'fragment length' to see if there is a different result, tweak the parameter '--extsize' while setting '--nomodel'.