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Search: Posts Made By: natpokah
Forum: Bioinformatics 05-27-2011, 10:52 AM
Replies: 25
Views: 14,909
Posted By natpokah
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...
Forum: Bioinformatics 05-27-2011, 10:27 AM
Replies: 25
Views: 14,909
Posted By natpokah
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...
Forum: Bioinformatics 05-27-2011, 10:19 AM
Replies: 25
Views: 14,909
Posted By natpokah
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...
Forum: Bioinformatics 05-27-2011, 06:41 AM
Replies: 25
Views: 14,909
Posted By natpokah
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...
Forum: Bioinformatics 05-25-2010, 11:28 AM
Replies: 2
Views: 4,024
Posted By natpokah
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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