unmapped reads with ssaha2

[sammy07]

Hi Moritz, unfortunately I can't help you, I didn't work with ssaha2 afterwards. You could possibly try BWA (BWA-SW) instead. Regards

[moritzhess]

Hi Sammy07,

could you already find out if ssaha2 (or anybody else) can output unmapped reads in sam format ?
I would also be very interested in such an option.

Moritz

[sammy07]

Hi everybody!

Does someone know how to make ssaha2 output unmapped reads (in the sam file format)? On their website they state that in the recent version, the sam output should contain unmapped reads (http://www.sanger.ac.uk/resources/software/ssaha2/, FAQ section); but according to the manual, this seems to apply only for paired-end reads. If thats not possible, what would be the easiest way to go through the reads-file and the sam-file and get the unmapped reads?

A second problem is that even using the -best option, ssaha2 outputs multiple alignments for the same reads if they have the same score. Is there an option to randomly choose one of these alignments; otherwise, what would be the easiest way to simulate this behavior? (It is surely possible to write a script that reads the sam file and randomly discards one of these alignments...)

Thanks in advance!