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Forum: General 11-17-2011, 11:48 AM
Replies: 0
Views: 2,011
Posted By haonmada
refGene.txt file

Hello All,

How can I generate a refGene.txt file for a region. This file is needed for the gsMapper software.





Thanks
O
Forum: Bioinformatics 05-10-2011, 09:07 AM
Replies: 7
Views: 3,863
Posted By haonmada
Thanks for the replies everyone! So far I...

Thanks for the replies everyone!

So far I have separated my sff file into shortreads(<200bp) and longreads(>200bp).

have run the bwa short read aligner on the shortreads and the long read...
Forum: Bioinformatics 05-04-2011, 12:31 PM
Replies: 7
Views: 3,863
Posted By haonmada
Thanks for the Info ketan_bnf! Yes I know...

Thanks for the Info ketan_bnf!

Yes I know about the "bwa bwasw" component of bwa. That is what confusing me at the moment.

As I mentioned in the post I have a mixture of short reads and long...
Forum: Bioinformatics 05-03-2011, 01:25 PM
Replies: 7
Views: 3,863
Posted By haonmada
using bwt to align 454 reads

Hello All,

First of all I am very new at this NGS sequence analysis.
I have a sff file generated by the 454 machine.
In it I have 500000 reads
200000 of them are <200bp
300000 of them are...
Forum: 454 Pyrosequencing 01-22-2010, 12:15 PM
Replies: 1
Views: 1,909
Posted By haonmada
gsMapper contigs

Hello All,

What does the lower case and upper case Letters in the contigs build by gsMapper represent?

Also, How is HCDiff (high confidence) variations differences determined?

Thanks
HA
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