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Question: Peak-Calling With Macs From .Bowtie File
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gravatar for Sébastien Vigneau
6.2 years ago by
Sébastien Vigneau • 10
Sébastien Vigneau • 10 wrote:
Hi, I have ChIP-seq alignment files in .bowtie format and would like to perform peak-calling using MACS. However, .bowtie format doesn't seem to be supported in Galaxy. Is there a way around to have MACS analyze these files within Galaxy, or is the only option to use MACS in command line? Thank you for your help! Sébastien
alignment bowtie • 1.5k views
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modified 6.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.2 years ago by Sébastien Vigneau • 10
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gravatar for Jennifer Hillman Jackson
6.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Sébastien, The tags/control input for MACS needs to be in SAM format. SAM is an output format option for Bowtie. I believe there are various scripts available on the web to do the conversion between .bowtie -> SAM/BAM, but these should be evaluated carefully and I do not think that they incorporate as much information as directly outputting BAM/SAM (at least not the few I took a look at). Conversion between BAM <-> SAM can be done within Galaxy, if you need to do that. A sample MACS workflow is in Protocol 3 here: http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.2 years ago by Jennifer Hillman Jackson ♦ 25k
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