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:
- cat all BED files into 1 BED file
- use bedtools to convert the BED file to BAM file
- 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?