This is probably really simple, but how do you go from a BED file of genomic features to a wiggle file which contains the number of features at a given position on the chromosome? So, every position in the wiggle file gives the total number of features that overlap with that position in the chromosome.
By the way... is there also a possibility to distinguish between the strands? With my script it's possible, but absolutely not memory efficient for a whole genome, when working with NGS data... but with genomeCoverageBed it's not doable, is it?
David, genomeCoverageBed has a -strand option so you can specify to check reads only from a single strand. Even if it didn't, one could just use awk to filter to a specific strand, then pipe to bedtools.
ah ok thx, didn't know that. But anyways, I always use a script, since I also want to normalize for multiple hits... I work with short RNAseq and there it happens a lot. And that is not possible with such tools.