Obtain counts for specific genes with ChIP-seq data without peak calling

Question

[marinamrbiotech]

Hello,

I was wondering if it is possible to obtain counts for an specific set of genes without doing peak calling. The idea will be to perform an alignment and then obtain the counts for the set of genes using for example featureCounts.

Thanks,

Marina.

Answer 1

[Papyrus]

Yes, this is often done. You typically have your BAM files and a custom file for your locations (e.g. a BED of gene or transcript coordinates, promoters, etc.), and the only thing you have to do is to convert your locations file into the SAF format which featureCounts uses. There are many answers detailing how to build it (see one, two). Also, you have featureCounts in the R package Rsubread if it's easier for you.

[marinamrbiotech]

Thanks a lot !! I thought that was mandatory to first obtain the peaks profile to then obtain the counts, but I will do it directly from the BAM files obtained from the alignment. Also, I always use gtf file format for featureCounts, but thank you for the recommendation.

[Papyrus]

Yes, that's because most of the pipelines you see in ChIP-seq focus on defining peaks (peak calling) and then doing downstream analyses on them. But you can even do differential analyses without prior peak calling, directly from the BAMS, e.g. with csaw.

[marinamrbiotech]

So, using featureCounts directly from the BAM file should be enough to obtain gene expression values ?

[Papyrus]

If you input BAMs from ChIP-seq, you will obtain read counts for your protein/factor at those regions, not gene expression values.

[marinamrbiotech]

Okey. I understand thank you so much !! :)