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Forum: Bioinformatics 04-10-2012, 10:44 AM
Replies: 4
Views: 1,298
Posted By hv4
Thank you for your feedback. @bioBob: ...

Thank you for your feedback.

@bioBob:

The program does not remove any reads. Just trims them.

You can use it with paired reads since the program does exactly the same thing
for both reads....
Forum: Bioinformatics 04-09-2012, 02:01 PM
Replies: 4
Views: 1,298
Posted By hv4
trimming bases

Hi,

When trimming reads I found Perl to be really slow for large files.

I wrote this C program to trim at the left and right ends.

Does this look OK to you?

#include<stdio.h>
Forum: Bioinformatics 10-29-2011, 02:21 PM
Replies: 2
Views: 3,731
Posted By hv4
Yes, that is correct the samples and the...

Yes, that is correct the samples and the reference contain all chromosomes.

The interesting thing is that I am running 8 samples in parallel and the results for all of them contain only chr1-3.
...
Forum: Bioinformatics 10-28-2011, 01:36 PM
Replies: 2
Views: 3,731
Posted By hv4
samtools mpileup

Hi,

I am using the following command

(samtools view -bS $prefix.out.sam > $prefix.out.bam
samtools sort $prefix.out.bam $prefix.out-sorted
samtools rmdup $prefix.out-sorted.bam ...
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