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:
At last, the result is a large BAM file and very time-consuming.
Does anybody know a easier way to do that?
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Hanfei Sun •
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.
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
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
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
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