Count number of reads in peaks?

[albireo]

Hi

I have single-end chip-seq reads mapped to hg19. I have called peaks and have a .bed output.

Is there a software that scans the intervals in the bed and, referencing the .bam alignment, outputs some statistics about the number of reads within each peak? For examples, how many reads contribute to each peak?

[turnersd]

I've used HTseq-count to do this, but you could probably use bedtools as well. To use HTSeq I had to do some awk'ing of the BED file to make it look like a GFF.

[albireo]

Thanks, looks like bedtools had exactly what I was looking for!

[rory]

The Bioconductor package DiffBind makes this very easy, have a look at the vignette.

[shi]

Hi

I have single-end chip-seq reads mapped to hg19. I have called peaks and have a .bed output.

Is there a software that scans the intervals in the bed and, referencing the .bam alignment, outputs some statistics about the number of reads within each peak? For examples, how many reads contribute to each peak?

You may use the featureCounts function in the Bioconductor package Rsubread to count the number of reads mapped to each peak. It is an extremely fast counting function.

Wei