Tools for binning aligned reads?

[DPCook]

Hi everyone,

Sorry if the answer exists somewhere, but I have tried searching and have had no luck finding the answer to a possibly naive question.

I'm simply looking for a way to bin aligned reads (or similar chr/start/end data) into user-defined bin sizes and output into a txt file with bin densities (chr/start-bin/end-bin/total read density in bin).

I also have density per base from bedtools genomeCov (chr/pos/density) and I'm curious how I could bin this format as well (ie. chr/start-bin/end-bin/total bin density).

Any help would be greatly appreciated,

David Cook

[Brian Bushnell]

If your data is currently in sam/bam, you can do that with BBTools' pileup.sh script:

pileup.sh in=mapped.sam out=stats.txt bincov=coverage.txt binsize=1000

That will give coverage within each bin. For read density regardless of read length, add the "startcov=t" flag.