MACS2 transcription start site analysis of .BAM files

Question

[carlee.bettler]

Hi! I'm new to using MACS2 and I would love some help :)

I have a .BAM file from an AF9 ChIP-Seq done with mouse (mm9 genome) cells. I'm trying to find binding sites -500 to +1kb from transcription start sites but I'm not sure how to do this.

Do I need to provide a second file with TSS locations for mm9? How do I even set the parameters for my command to have a start and end point? Is MACS2 even the best software for this task (maybe Homer would better)?

Thank you so much!

Answer 1

[ATpoint]

Run macs as usual to obtain a peak file (narrowPeak format). Make a BED file with your TSS coordinates. Use bedtools intersect to extract peaks overlapping the TSS coordinates. By the way, if you have no legacy burden change to mm10, mm9 is very old and there is no reason to use it unless your project relies on legacy / previous data on mm9.

[carlee.bettler]

Thank you! Unfortunately I had to duplicate some research to get my .bam file that used mm9 :/