Currently I'm working with BLAT alignment data downloaded from UCSC browser and own generated alignment data using GMAP.
In the next few weeks I want to give the big next steep to work with RNAseq row data. I'm basically interested to study the splice junction (canonical and non-canonical).
I want to test the memory-eficents and fast RNAseq alignment programs. My candidates are:
- BLAT (for the 100 bp reads RNAseq data)
I read the GSNAP paper and it's looks very promising, but I didn't found commentaries about it. Anybody tried it?
Anyway, What others programs do you advice to test?
Thanks for your time!