ChIP-seq Peak calling from BED or WIG file
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Entering edit mode
9 weeks ago
gspirito ▴ 10

Hello everyone, here's my question:

I retrieved ChIP-seq data from ENCODE (bed and wig format):

https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM772833&format=file&file=GSM772833%5FBI%2EBrain%5FMid%5FFrontal%5FLobe%2EH3K27me3%2E149%2Ebed%2Egz https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM772833&format=file&file=GSM772833%5FBI%2EBrain%5FMid%5FFrontal%5FLobe%2EH3K27me3%2E149%2Ewig%2Egz

The bed files contains information about all mapped reads (~25 millions):

chr1 9985 10184 B09EJABXX110518:6:1105:16310:167305 0 -

chr1 9997 10196 B09EJABXX110518:6:2208:11946:182038 0 -

chr1 12882 13081 B09EJABXX110518:4:1107:18270:92118 0 -

.....

How would I convert one of these two files (either the bed or the wig) to a bed file containing the coordinates of the peaks?

Thanks in advance.

ENCODE ChIP-seq • 185 views
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Entering edit mode
9 weeks ago
ATpoint 55k

Peak callers such as macs can use BED files that contain read coordinates to return peak lists.

Something basically like:

https://github.com/macs3-project/MACS

macs2 callpeak -t that_bed_file.bed -f BED
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