Forum: Bioinformatics
09-03-2013, 04:46 PM
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Replies: 3
Views: 1,555
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Forum: Bioinformatics
09-09-2012, 09:35 PM
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Replies: 6
Views: 3,824
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Forum: Bioinformatics
05-21-2012, 05:02 PM
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Replies: 3
Views: 2,834
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Forum: Bioinformatics
09-05-2011, 06:49 PM
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Replies: 6
Views: 5,025
OrthoMCL duplicate entry error
I have made it up to step 10 of the orthomcl process, finding protein pairs, but have become stuck with a duplicate entry error:
Duplicate entry '5206|CNAG_00003-5206|CNE00390' for key...
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Forum: Bioinformatics
08-23-2011, 09:01 PM
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Replies: 10
Views: 9,063
I have run it and got a few of those errors. It...
I have run it and got a few of those errors. It still completed though and I've compared the results with what I found with BreakDancer - didn't find anything new, BreakDancer picked up around 80%...
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Forum: Bioinformatics
08-17-2011, 04:48 PM
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Replies: 5
Views: 3,193
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Forum: Bioinformatics
08-15-2011, 05:48 PM
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Replies: 2
Views: 3,119
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Forum: Bioinformatics
08-14-2011, 07:31 PM
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Replies: 2
Views: 3,119
CREST/perl module Tree::Interval
I'm trying to run CREST (http://www.stjuderesearch.org/site/lab/zhang) but it is trying to locate a perl module Tree::Interval which I have had no luck finding anywhere. Does anyone know where I can...
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Forum: Genomic Resequencing
07-10-2011, 03:22 PM
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Replies: 27
Views: 17,436
Did you try FreeBayes? I'm facing this problem...
Did you try FreeBayes? I'm facing this problem now and wondering what to use. I've tried GATK and it does appear to work (very superficial examination) but am concerned there might be issues I'm...
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Forum: Bioinformatics
04-19-2011, 08:03 PM
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Replies: 6
Views: 3,960
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Forum: Bioinformatics
04-11-2011, 04:46 PM
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Replies: 9
Views: 2,836
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Forum: Bioinformatics
04-10-2011, 09:26 PM
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Replies: 5
Views: 3,193
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Forum: Bioinformatics
04-10-2011, 08:15 PM
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Replies: 5
Views: 3,193
RepeatMasker output
Where is the output from RepeatMasker saved? I can see the temporary folder in my directory during running but it disappears when it finishes and I can't find a *.masked file anywhere! Is there a...
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Forum: Bioinformatics
04-01-2011, 07:17 PM
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Replies: 3
Views: 2,834
BWA errors after quality trimming
After I use the "-q 20" option in bwa aln I start getting errors down the road eg when i run ValidateSamFile in picard I get lots of "Mate negative strand flag does not match read negative strand...
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