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Thursday, October 9, 2008

Maq .map to .bed format converter

I've finally "finished" the manual for one section of the Vancouver Short Read Analysis Package - though it's not findpeaks. (I'm still working on that - but it's a big application.) It could still use pictures and graphs, and stuff... but it's now functional.

One down... about 7 more manuals to write. Documentation is never the fun stuff.

What slowed this down, ironically, was my inabilty to read the Maq documentation. I completely missed the fact that unmapped reads are now included in PET aligned .map files, but with a different paired flag status. Previously, unmapped ends were thrown away, and I had to handle the unpaired ends. With the new version, those unmapped reads are now included, but given a status of 192, so they can be paired again - albeit there's not much information in the pairing. Infact, I can even handle the other ends as I find them, because they're given a status of 64. (Do these numbers seem arbitrary to anyone other than me?)

Anyhow, Finally, the .map to .bed converter works - and there's a manual to go with it.


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