alignment software and ref sequence

[mlee]

We are currently using MAQ to align our Solexa reads to our reference sequence. Does anyone know if MAQ can also tell me which parts of my reference sequence have no reads aligned to them? If not, can anyone suggest a program that can tell me this info? Thanks!

[spenthil]

Pretty sure MAQ can't, and a quick scan of the man page didn't yield anything.

Have you tried one of the visualization tools? Only one I know off the top of my head is tablet, but unfortunately haven't had a chance to play with it myself:

http://bioinf.scri.ac.uk/tablet/index.shtml

[dnusol]

Actually, if I am not wrong, Maq`s pileup output has a column with the number of reads aligning at a given position, so you can get those with a 0 coverage out

HTH,

Dave

[BaCh]

We are currently using MAQ to align our Solexa reads to our reference sequence. Does anyone know if MAQ can also tell me which parts of my reference sequence have no reads aligned to them? If not, can anyone suggest a program that can tell me this info? Thanks!

MIRA does. Can even give back a list of genes and/or intergenic regions which are hit by this (if references sequence has annotations like, e.g., a GenBank). If you're working with 20 to 30m reads, have a look at it.

Beware, being a de-novo assembler, it's a lot more memory intensive than other mapping programs when used for mapping only.

Regards,
B.

Disclaimer: I wrote MIRA. It's useful to me but it might not be for you. Feedback appreciated.