Question: Peak Calling on BED files
gravatar for VY
2.2 years ago by
United States
VY120 wrote:

This is somewhat of a naive question.

I've been using MACS2 on galaxy to call peaks on my ChIP-seq BAM. files as is the usual. 

Recently though I performed the MACS2 filterdup function, to filter out any duplicates I have; this outputs BED. files of my reads.

Is it okay to use the BED. Files to call peaks or should I convert the BED. files to BAM. and then run MACS2?


Thanks in advance for your help.

macs2 chip-seq • 1.3k views
ADD COMMENTlink modified 2.2 years ago by Jennifer Hillman Jackson24k • written 2.2 years ago by VY120
gravatar for Jennifer Hillman Jackson
2.2 years ago by
United States
Jennifer Hillman Jackson24k wrote:


BED format is fine for input. This tool filters for appropriate datatypes in the input section of the tool form (as many Galaxy wrapped tools do). 

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 2.2 years ago by Jennifer Hillman Jackson24k
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