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nataliesilmon 12-09-2015 06:42 AM

Next gen sequencing analysis - for small genomes

I am working on an organism with a small genome (Toxoplasma gondii, 65 Mbp). With ChIP-seq, we naturally tend to get very high sequence coverage compared to human/mouse/organisms with large genomes. Since low sequencing depth and coverage can influence ChIP-seq analysis, what is the impact of high or over sequencing? Does this influence peak calling and IDR analysis? (especially since these tools were designed and tested using data from mammalian cells where there is lower coverage compared to small genomes). Are there any considerations that I should make while using e.g. MACS2 and the ENCODE IDR pipeline with a smaller genome?

Thank you very much for any advice.


SylvainL 12-10-2015 01:14 AM

With MACS, you have to give the genome size...

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