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Forum: Bioinformatics 07-13-2010, 09:50 AM
Replies: 10
Views: 5,391
Posted By stubrown
OK, that was a very helpful idea to work with the...

OK, that was a very helpful idea to work with the index of just one chromosome. That worked fine. So I guess my problem is really about how do I index an entire genome of chromosome *.fa files? (i.e....
Forum: Bioinformatics 07-13-2010, 07:18 AM
Replies: 10
Views: 5,391
Posted By stubrown
Need workflow from SRA to BreakDancer

I am flummoxed by "fastq" formats. My goal for the moment is to test out BreakDancer to find translocations at low coverage. I don't have our own data yet, so want to use data from SRA. I have...
Forum: Illumina/Solexa 08-24-2009, 12:34 PM
Replies: 18
Views: 5,928
Posted By stubrown
We are just getting started with the RNA-seq kits...

We are just getting started with the RNA-seq kits on Illumina GA, but I have seen stacks like these in ChIP-seq experiments. I think they are due to PCR amplification bias (some templates amplify...
Forum: Illumina/Solexa 11-17-2008, 09:45 AM
Replies: 1
Views: 4,894
Posted By stubrown
Need Phix control sequence.txt

We just lost all our raw and archived Solexa data in a stupid SAN controller crash. :mad:

Not a scientific disaster, but I have a student who is working on a statistical analysis of coverage vs...
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