Forum: Bioinformatics
05-27-2011, 10:52 AM
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Replies: 25
Views: 14,909
Yeah, the only reason to remove the reads with...
Yeah, the only reason to remove the reads with too many N before aligning was for our statistics down the line. We wanted to have meaningful % of unique match. And since sometimes the fastq comes...
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Forum: Bioinformatics
05-27-2011, 10:27 AM
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Replies: 25
Views: 14,909
Hi again!
So, -A worked wonders! Thank you! ...
Hi again!
So, -A worked wonders! Thank you!
Would the fact of sorting the fastq by ID name help speed up even more?
Also, since I filter reads that have to many "N" and I trim the adaptors, one...
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Forum: Bioinformatics
05-27-2011, 10:19 AM
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Replies: 25
Views: 14,909
Hi there!
Thanks for a quick reply!
You are...
Hi there!
Thanks for a quick reply!
You are totally right, the insert size estimate is huge and then sampe gets stuck hours trying to "align unmapped mate".
I will follow your advice and try the...
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Forum: Bioinformatics
05-27-2011, 06:41 AM
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Replies: 25
Views: 14,909
bwa sampe very slow
We are trying to run sampe on sai files generated from fastq files obtained with hiseq2000. There is about 100 million pair ended 104 bases reads.
we have estimated insert size at about 200 to 500...
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Forum: Bioinformatics
05-25-2010, 11:28 AM
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Replies: 2
Views: 4,024
Bowtie, Tophat and Python
Dear all,
I installed bowtie 0.12.5, tophat 1.0.13 and I have Pyhton 2.4 on my Linux.
When I launch tophat with the test files downloaded from their websites, I get this error message
$...
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