Homopolymers // ValleyFilters

[Splinter479]

Hi,
I got a 454 sequencing run of a rabbit virus and it seems very crappy. I have no idea why,
the filters are all set on default as usual.
Of cause the first suspects are homopolymers. I am pretty new to 454 sequencing so I don't know how to proove it. Are there any helpful statistics in the gsRunBrowser or usable files in the project folder where I should have a look at?
Furthermore I found a GC-rate at almost 70%, seems not normal, isn't it?

Thanx a lot.

[colindaven]

You don't provide enough information to help.

-is this a de novo or reference mapping analysis ?
-what GC do you expect the virus to have ? Check the GCs of related viruses in Genbank.

I can't imagine 454 homopolymers would significantly change the GC - they didn't in my data.

Good luck