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Forum: Bioinformatics 04-06-2010, 03:25 PM
Replies: 0
Views: 1,049
Posted By julien
Pileup decoding issue ("]" symbol)


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
Views: 4,742
Posted By julien
how critical is the filtering of potential PCR duplicates?


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
Views: 1,980
Posted By julien
Pileup to contig

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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