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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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Possible option: generate bedGraph without peaks #143

Open ghost opened 8 years ago

ghost commented 8 years ago

Hello,

I am interested in generating signals, and as I understand to do that I need to have files in bedGraph format. I understand that to generate bedGraph files I need to call callpeaks, however, I do not want to calculate peaks, just would like to have bedGraph files to generate signals.

As I got from your code (maybe I am wrong), the transformation of replicate and control files to bedGraph is executed before peak is calculated, at least, for each chromosome. So, is that possible to add an option, which allows to skip the part of calculating peaks and just save bedGraph files to generate signals.

I am sorry if I missed something and this option already exists.

Sincerely, Jurijs Nazarovs

taoliu commented 8 years ago

Hi Jurijs,

How about this: https://github.com/taoliu/MACS/wiki/Advanced%3A-Call-peaks-using-MACS2-subcommands

From step1 to step6.

Best, Tao

ghost commented 8 years ago

Hi Tao,

Thanks for the response, the provided manual is useful. However, during the stages: slocal and llocal backgrounds, once I use "$ macs2 bdgopt -i 1k_bg.bdg -m multiply -p 0.254 -o 1k_bg_norm.bdg" (with my names and numbers), I get the following error: File "MACS2/IO/BedGraph.pyx", line 830, in MACS2.IO.BedGraph.bedGraphTrackI.apply_func (MACS2/IO/BedGraph.c:11540) TypeError: 'float' object has no attribute 'getitem'

I am not sure why it appears, but it would be great if you can help with that.

Sincerely, Jurijs Nazarovs