Using MACS for Mitochondrial Genome

Question

[ndd25]

I am interested in analyzing ChIP-seq data for 183 oocyte samples using macs14. However, I am very interested in the mitochondrial interaction with the chosen TRX factors. When I align my fasta files with the mitochondrial genome and perform a NUMT analysis I then try to use this bam file for macs analysis. I have tried numerous different manipulations of my initial sam file and have been unable to call any peaks. It seems that there is too much background noise to be able to call the peaks. From what I've read, chrM is normally excluded for macs analysis and could be too small with too many reads to work. Is it at all possible to use chrM only alignments for ChIP-seq data? Does anyone have a definitive answer?

Answer 1

[Ian]

I have answered a similar question to this before:

Chip-Seq For Mitochondrial Genes

I think the first approach is to reduce --slocal and --llocal (lambda params) or perhaps use a fixed background --nolambda. Not sure, but its worth a go.