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Forum: Bioinformatics 08-24-2011, 07:41 AM
Replies: 17
Views: 13,167
Posted By TuA
Thanks for that input rskr!:)

Thanks for that input rskr!:)
Forum: Bioinformatics 08-24-2011, 07:05 AM
Replies: 17
Views: 13,167
Posted By TuA
Thanks everyone for your suggestions! I...

Thanks everyone for your suggestions!

I played around with samtools quite a bit now, but didn't get really satisfying results. At the moment I'm therefore a bit suspicious of using samtools for...
Forum: Bioinformatics 08-15-2011, 02:58 AM
Replies: 17
Views: 13,167
Posted By TuA
Question samtools mpileup calls way too less SNPs

Dear all,

For some reasons I get way too less SNPs called with samtools mpileup (0.1.17) that I'm supposed to get.

I work with paired-end SOLiD data (partial genome resequencing of a diploid...
Forum: Bioinformatics 05-27-2011, 08:32 AM
Replies: 5
Views: 10,160
Posted By TuA
Hi tldgID Sorry for not responding earlier....

Hi tldgID

Sorry for not responding earlier. I'm afraid I don't think the data will be of use for you. I actually downloaded data from different projects on mammals but with only 1-2 samples per...
Forum: Bioinformatics 05-27-2011, 08:31 AM
Replies: 5
Views: 10,160
Posted By TuA
Hi tldgID Sorry for not responding earlier....

Hi tldgID

Sorry for not responding earlier. I'm afraid I don't think the data will be of use for you. I actually downloaded data from different projects on mammals but with only 1-2 samples per...
Forum: Bioinformatics 05-23-2011, 04:07 AM
Replies: 5
Views: 10,160
Posted By TuA
This is great! Thanks a lot! I'll check what my...

This is great! Thanks a lot! I'll check what my machine can do ;-)
Forum: Bioinformatics 05-23-2011, 02:15 AM
Replies: 5
Views: 10,160
Posted By TuA
Question How convert multiple .sra files into .fastq in one go?

Hi all,

I have hundreds of .sra files of a genome re-sequencing project which I downloaded from the NCBI sequence read archive. Does anyone know a quick way of converting them into fastq files?...
Forum: Bioinformatics 05-23-2011, 01:17 AM
Replies: 5
Views: 3,929
Posted By TuA
Thanks for your help! I'll give it a try...

Thanks for your help! I'll give it a try...
Forum: Bioinformatics 05-16-2011, 03:57 AM
Replies: 5
Views: 3,929
Posted By TuA
Thanks Simon for your helpful post. It seems to...

Thanks Simon for your helpful post. It seems to be pretty time intense to create these liftOver chain files. Do you have any experience on the accuracy, i.e. how well the coordinates can be...
Forum: Bioinformatics 05-10-2011, 12:30 PM
Replies: 5
Views: 3,929
Posted By TuA
Post How to convert genome coordinates from two assemblies

Hi!

Iím working with two closely related species ( < 1 MY) and got a reference genome for both of them. I re-sequenced several individuals per species and mapped the reads to the reference genome...
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