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 On 9/11/12 3:26 PM, Sébastien Vigneau 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

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