Binning of aligned mRNA-reads into gene models

[jwaage]

Hi all,

After mapping our mRNA-reads to the genome, I've been relying on the INNER-JOIN function of UCSC Galaxy to hook my mapped reads up to exons, introns, intergenic areas and so on... As uploading large files to Galaxy is a pain in the %€$ (at least from Europe), and as we don't have a local mirror yet, I would like to ask if anyone knows of a script / program (perl, c, python) that does this quickly? Basically it's a simple interval overlap problem, but it seems to be multiplicative in terms of CPU usage..

Thx in advance,
JW, Cph. Uni

[kopi-o]

In case all you want is interval overlaps, no more no less (well, except for some features like extending the intervals etc.), I have found fjoin (written in Python) to be a fast and simple tool. The download link is ftp://ftp.informatics.jax.org/pub/fjoin

You could also try cisGenome (http://www.biostat.jhsph.edu/~hji/cisgenome/) which has lots of different tools for this kind of task.