Getting the part of a genome that was NOT covered by a samples reads

[naymikm]

I have a bunch of genomes and sample reads and am looking for a way (software and method) that I can do a sequence alignment and get an output of the part(s) of the genome that were NOT covered by the sample reads. Any Ideas?

[Bukowski]

Do the alignment and then use genomecov from bedtools:

http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html

[rnaeye]

You can use bedtools too calculate genome coverage. Here is an example:
http://genescripts.com/index.php/9-n...enome-coverage

[mchizar]

DNASTAR's SeqMan NGen will automatically create features in regions where there is no coverage as well as a coverage report that lists these regions. They also have a autoscripting tool, SeqNinja that can create new sequences from these "coverage" features.

[naymikm]

I just realized I never thanked you all for the help! Actually, the project that I was working on here lead to my senior research project and eventually my acceptance into graduate school! I thank you all for your help!

Marcus