Identify Summit Positions From Bed File

Question

[Vikas Bansal]

Dear all,

I have ~40k coordinates in bed file and I want to identify summit coordinate for each of them. I have mapped file with ~8 million reads mapped, also in bed file. I found Identifying The 'Summit' Coordinate Within Many Coordinates In A Wig File? post but one of the solution is with the Python and it was asked 2 years ago. Does anybody know a tool (is it possible with bedtools or BEDOPS?) which can solve this problem quickly?

Best wishes, Vikas

Answer 1

[KCC]

It turns out macs could be the answer here. The newest version of macs, macs2 has an option called refinepeaks. This is a functionality independent from the peak caller.

usage: macs2 refinepeak [-h] -b BEDFILE -i IFILE
                        [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
                        [-c CUTOFF] [-w WINDOWSIZE] [-o OPREFIX]
                        [--verbose VERBOSE]

The BEDFILE here is the list of peak calls.

This is the description: "(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags"

The way it refines the summits is to look at tags on the forward reverse strands similar to the way SPP works. So, it's not a simple algorithm that locates the maximum value and spits that out. This method of comparing the forward and reverse strands works best for transcription factors.

[Vikas Bansal]

Thanks for the reply. I think it refines somehow for the chip seq data. But my file has nothing to do with the chip seq.

[KCC]

I agree it's designed for ChIP-seq, in that it assumes that there will be patterns in the reads that are assigned to the forward and reverse strands. I think it should work for sequencing data with punctate peaks (so sharp peaks) where the tags have equal probability of occurring on both strands.

Answer 2

[sirenbeserker]

If you use MACS for peak finding, it will report the summit coordinates.

[Vikas Bansal]

Thanks for the reply. I know that but I am not using MACS. I just got this file from somewhere else.