Question: Peak-Calling With Macs From .Bowtie File
gravatar for Sébastien Vigneau
6.2 years ago by
Sébastien Vigneau10 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
ADD COMMENTlink modified 6.2 years ago by Jennifer Hillman Jackson25k • written 6.2 years ago by Sébastien Vigneau10
gravatar for Jennifer Hillman Jackson
6.2 years ago by
United States
Jennifer Hillman Jackson25k 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: Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 6.2 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 177 users visited in the last hour