Gmap Output Statistics

Question

[Damian Kao]

Is there anyway to get some kind of mapping score statistic from GMAP output? A score similar to e-value or mapping quality. It seems like the threshold values used in their oligomer chaining alignment algorithm are hard coded into the software?

Has anyone turned on the --nosplicing flag and used GMAP for aligning genomic sequences instead of mRNA/EST? How does it perform?

Answer 1

[Ying W]

Did you check the sam file for mapping quality? The readme states that mapping quality is stored in an XQ flag

I could not find anything in the readme about the --nosplicing flag. I would probably make GMAP run faster, however, one of the advantages of using GMAP is how well it handles splicing events. If you did not need this functionality, other mappers might be more suitable for you and faster (such as bowtie).