Forum: Bioinformatics
08-14-2013, 06:42 PM
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Replies: 1
Views: 1,037
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Forum: Bioinformatics
10-26-2012, 12:48 PM
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Replies: 4
Views: 2,886
Hi swbarnes2,
Here is my output in the...
Hi swbarnes2,
Here is my output in the MarkDuplicates metrics file:
## METRICS CLASS net.sf.picard.sam.DuplicationMetrics
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED ...
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Forum: Bioinformatics
10-26-2012, 10:37 AM
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Replies: 4
Views: 2,886
Hi vivek,
BAM flags won't work for this. ...
Hi vivek,
BAM flags won't work for this. The information about the paired read does not tell you anything about whether the read is still in the file. It only contains information about its...
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Forum: Bioinformatics
10-26-2012, 08:48 AM
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Replies: 4
Views: 2,886
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Forum: Bioinformatics
10-23-2012, 10:44 AM
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Replies: 15
Views: 8,172
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Forum: Bioinformatics
10-22-2012, 11:37 AM
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Replies: 8
Views: 2,703
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Forum: Bioinformatics
10-22-2012, 11:00 AM
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Replies: 8
Views: 2,703
Hi cwhelan,
I do want to see how many...
Hi cwhelan,
I do want to see how many supporting reads for each SV call come from each library. However, the output I have generated using bam2cfg.pl followed by breakdancer_max on a merged bam...
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Forum: Bioinformatics
10-15-2012, 08:26 AM
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Replies: 8
Views: 2,703
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Forum: RNA Sequencing
07-07-2012, 10:23 AM
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Replies: 1
Views: 1,865
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Forum: Bioinformatics
05-18-2012, 08:39 AM
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Replies: 3
Views: 2,847
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Forum: Bioinformatics
05-18-2012, 07:20 AM
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Replies: 3
Views: 4,689
Rocketknight,
After thinking about it...
Rocketknight,
After thinking about it further, I think your right. Ultimately, it seems like the empirical mismatch rate would be higher for any class of mutations (possibly including the class...
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Forum: Bioinformatics
05-17-2012, 12:35 PM
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Replies: 3
Views: 4,689
Hi Rocketnight,
A little late on the reply,...
Hi Rocketnight,
A little late on the reply, but I'm contemplating some of these issues myself. The mutation bias issue you mentioned seems like it might be a problem only if this class of...
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Forum: Bioinformatics
05-17-2012, 11:58 AM
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Replies: 15
Views: 11,040
There is a suggested method for non-model...
There is a suggested method for non-model organisms (without a snp db) on the GATK wiki:
http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration
The proposed method is...
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Forum: General
05-15-2012, 09:29 AM
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Replies: 0
Views: 1,325
Is GATK Indel Realigner read group aware?
Hello,
I want to realign a multi-sample BAM using the Indel Realigner for eventual SNP-calling. I am following the GATK's "Best Practice Variant Detection with the GATK version 3" which recommends...
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Forum: Bioinformatics
03-26-2012, 08:19 AM
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Replies: 5
Views: 3,988
That is not necessarily true. If you have...
That is not necessarily true. If you have aligned your data with BWA then the recommended way to get "unique" reads (by Heng Li) is to filter on map quality. See the samtools FAQ under the section...
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Forum: Bioinformatics
03-20-2012, 12:12 PM
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Replies: 4
Views: 1,983
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Forum: Bioinformatics
03-19-2012, 12:11 PM
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Replies: 4
Views: 1,729
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Forum: Bioinformatics
03-19-2012, 12:00 PM
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Replies: 20
Views: 3,298
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Forum: Bioinformatics
03-19-2012, 10:51 AM
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Replies: 20
Views: 3,298
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Forum: Bioinformatics
03-16-2012, 01:38 PM
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Replies: 1
Views: 4,448
BWA aligned pairs read1=XT:A:U, read2=XT:A:R
Hello,
I've aligned Illumina paired end reads with BWA, filtered using samtools view -f 3 -F 12 ("proper pairs", both mates mapped).
I'm looking at the XT tags and see expected classes, where...
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Forum: Bioinformatics
03-13-2012, 11:56 AM
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Replies: 11
Views: 3,564
Good, at least now youre not filtering out the...
Good, at least now youre not filtering out the homozygous sites.
If you follow the example carefully from the biostar-exchange link I sent you, you will see that the genotypes (e.g., 0/0,0/1,1/1)...
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Forum: Bioinformatics
03-12-2012, 01:35 PM
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Replies: 11
Views: 3,564
One final parting shot, given that Heng Li has...
One final parting shot, given that Heng Li has indicated that there is a problem with the genotypes in the vcf (see example at http://biostar.stackexchange.com/que...quality-scores) I would hesitate...
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Forum: Bioinformatics
03-12-2012, 01:29 PM
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Replies: 11
Views: 3,564
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Forum: Bioinformatics
03-12-2012, 09:03 AM
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Replies: 4
Views: 2,304
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Forum: Bioinformatics
03-12-2012, 07:11 AM
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Replies: 13
Views: 4,704
Hi swbarnes2,
Just wanted to follow up on...
Hi swbarnes2,
Just wanted to follow up on the issue of generating multiple consensus sequences from mpileup run with multiple BAMs in the event that someone happend upon this thread with the same...
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