How To Pile Up Multiple Bed Files Into 1 File

Question

[Hanfei Sun]

I want to pileup a set of BED files (all from H3K4me3) to see some generic site of this Histone Modification.

However, I haven't found a suitable tool to do that..

I'm using a awkward way to do that, like this:

1. cat all BED files into 1 BED file
2. use bedtools to convert the BED file to BAM file
3. use samtools' mpileup command to pileup the BAM file

At last, the result is a large BAM file and very time-consuming.

Does anybody know a easier way to do that?

Answer 1

[Madelaine Gogol]

You could use pipes to help with streamlining the steps, if you're not already. You could try bedtools genomeCoverageBed to do the pileup instead of samtools.

Answer 2

[Mary]

Do you want to do a display like they have for the histone modifications on the UCSC browser now? Those are called "multi wig". See if this info helps: http://biowhat.ucsd.edu/homer/ngs/ucsc.html

[Hanfei Sun]

No, it's not multiple wiggle file. It's multiple BED file. I just want to find some peaks appears in most of the H3K4me3 samples

Answer 3

[Alex Reynolds]

The BEDOPS tool called bedops will merge your BED data for you:

$ bedops --everything *.bed > merged.bed

You could convert data faster by piping output to bed2bam, which supports standard input:

$ bedops --everything *.bed | bed2bam -a stdin -g chrlist.txt > merged.bam