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Forum: Bioinformatics

04-06-2010, 03:25 PM

Replies: 0

Pileup decoding issue ("]" symbol)

Views: 1,047

Posted By julien

Pileup decoding issue ("]" symbol)

Hi,

I was wondering if someone encountered this problem with their pileups.

In the example bellow:
2L 9889 A A 102 0 55 25 ,.,,,,,,,,,..,.,,,,..,,^,.^]. F>HHFFFEG:EHHHFFGF#IIEECH

1- I...

Forum: General

01-18-2010, 11:53 AM

Replies: 3

how critical is the filtering of potential PCR duplicates?

Views: 4,735

Posted By julien

how critical is the filtering of potential PCR duplicates?

Hello,

I don't really have a good appreciation for how critical it is to remove potential PCR duplicates from the alignments (either via samtools rmdup or picard). It would appear (based on posts...

Forum: Bioinformatics

11-22-2009, 10:26 PM

Replies: 2

Pileup to contig

Views: 1,974

Posted By julien

Pileup to contig

Hi,
I was wondering if any of you know of, or have a script to go from a pileup to series of contigs? It seems like the easiest way to get contigs from a BWA alignment but maybe someone has a...

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