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crazyhottommy / ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang
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Missing summit location when run macs2 with --broad option #6

Closed AlicePsyche closed 6 years ago

AlicePsyche commented 7 years ago

Hi, tommy

Thanks for your post about MACS, it helps me a lot!

Actually I usually use Homer to call histone modification peaks. Recently, I need to use macs to "validate" my previous results. When I run 

macs2 callpeak -t test_rep1.bam -n test --broad -p 0.01 --nomodel --extsize 147 -g 1.4e9

The output files don't have NAME_summits.bed and there is no column of "absolute peak summit position" in NAME_peaks.xls. Did I miss some specific options?

Or do you happen to know how can I quickly identify the summit location in a bed file(The most enriched signal location in a region)? I am new to bioinformatics, I write a small script to calculate the 100bp bin region FPKM then screen the max value...but it is very slow(of course)..

Thanks for your help in advance!

crazyhottommy commented 7 years ago

it seems if you specify --broad, no summit will be reported by macs2. The only way to do is get a single base pair pipleup say by bedtools genomcov and then for each broad peak identified by macs2 check with base has the highest value.

I also see you asked the question on the pybigwig page. as you see, there is no direct way you can get it easily...

AlicePsyche commented 7 years ago

Thanks for your reply! Kind of desperate...I also asked the questions on biostar, macs, Homer 😅 New to bioinformatics, just intuitively thought it was a simple question but I could not find more elegant solution. (￣o￣)

Thanks again, your series of ChIP-seq blog really help me a lot.

crazyhottommy commented 7 years ago

glad it helps! I was new too, that's why I wrote down the notes.