Question: ChIP-seq analysis on small genome
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Randy • 0 wrote:
Hello, I am using Galaxy to analyze ChIP-seq data of a mammalian cell line containing virus episome. I could map reads to both hg19 and virus genome, separately, with Bowtie2. Also I could find peak on hg19 with MACS2. However, I was not able to search peak on virus genome with MACS2, although I changed effective genome size to 138,000 bp, the size of virus genome. MACS2 just stop and could not process it. Wonder to know how to modify the parameters to make MACS2 work on small genome? Thank you very much for the help in advance! Randy
Hi Randy - I haven' t personally tuned MACS2 for a viral genome, but perhaps others have and can offer advice, so I will just comment so the post stays open. That said, this is where I would look for info on the web. - Jen, Galaxy team