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CCBR / CARLISLE

Cut And Run Analysis Pipeline
https://ccbr.github.io/CARLISLE/
MIT License
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use summit.bed file as input for homer #105

Closed slsevilla closed 9 months ago

slsevilla commented 10 months ago

Describe what enhancement you'd like to see. Yue has requested that the input for homer is changed to the _summit.bed file. This is being generated during the MACS2 run, but is not being saved.

This is the recommended file from MACS2 documetation:

c. NAME_summits.bed

This is in BED format, which contains the peak summits locations for every peak. The 5th column in this file is -log10pvalue the same as NAME_peaks.bed. If you want to find the motifs at the binding sites, this file is recommended. The file can be loaded directly to UCSC genome browser. Remove the beginning track line if you want to analyze it by other tools.
slsevilla commented 9 months ago

completed with commit e2a9a7d7593e9ab48c90bae9de90e2ad87ab9338