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Question: Peak Calling on BED files
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gravatar for VY
2.9 years ago by
VY • 120
London
VY • 120 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 • 1.8k views
ADD COMMENT • link •
modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by VY • 120
0
gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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