Chip-Seq - How to do Quantile normalization on bam files?

Question

[ej]

Hi,

I am working with ChIP-Seq data and am interested in doing quantile normalization.

I created bedgraph files from my bam files using bamCoverage with a window size of 50 bp so that I get the number of reads for every 50 bp of genome. However I noticed that every bam file has a different number of lines (even after I split up the intervals that bamCoverage automatically merged) so I cannot use this for quantile normalization.

Now I am using bedtools multicov with a bed file I created with 50 bp windows across the genome (using bedtools makewindows) and my bam files to get read counts for all of my bam files using the same intervals but it is taking a long time to run.

I am wondering if there is a simpler, faster way to use quantile normalization with bam files for ChIP-Seq analysis.

Any help would be appreciated,

Thank you,
ej

Answer 1

[James Ashmore]

By default bamCoverage does not report bins with zero counts - this may be the reason why you are getting different number of lines reported. Instead of running bedtools multicov, you could run bedtools coverage on each of your samples in parallel, then merge them into one large count matrix.

[ej]

Thank you so much