Forum: Bioinformatics
11-17-2015, 03:11 AM
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Replies: 9
Views: 4,933
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Forum: Metagenomics
06-04-2015, 11:39 PM
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Replies: 5
Views: 2,727
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Forum: Metagenomics
06-04-2015, 05:48 PM
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Replies: 5
Views: 2,727
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Forum: Metagenomics
06-01-2015, 08:26 PM
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Replies: 5
Views: 2,727
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Forum: Bioinformatics
05-19-2015, 05:52 PM
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Replies: 1
Views: 1,707
The answer is it depends. Note that they use a...
The answer is it depends. Note that they use a very different statistical model, so it's not fair to compare the p-values. You'll have to understand the statistical model before you can conclude...
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Forum: Bioinformatics
05-19-2015, 05:47 PM
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Replies: 3
Views: 1,099
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Forum: Bioinformatics
05-18-2015, 05:28 AM
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Replies: 4
Views: 1,559
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Forum: Bioinformatics
05-18-2015, 12:02 AM
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Replies: 4
Views: 1,559
There is a nice example in the vignette. What...
There is a nice example in the vignette. What don't you give it a go? Put your commands here if you got stuck. Basically, you'll need to read in your count matrix file and specify the meta-data for...
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Forum: Bioinformatics
05-12-2015, 07:06 PM
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Replies: 14
Views: 4,763
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Forum: De novo discovery
05-12-2015, 06:59 PM
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Replies: 7
Views: 5,155
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Forum: Bioinformatics
05-11-2015, 12:13 AM
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Replies: 19
Views: 141,433
N50 is a good but not perfect statistic to...
N50 is a good but not perfect statistic to measure how well a de-novo assembly it is. We prefer a set of large contigs because they give us better confidence. This statistics tells us that.
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Forum: Bioinformatics
04-08-2015, 04:30 AM
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Replies: 4
Views: 2,923
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Forum: Bioinformatics
04-08-2015, 04:25 AM
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Replies: 0
Views: 1,371
Bug? Do we need a header for a SAM?
I'm using the htslib C library for parsing my SAM files (also used by the samtools project). The library fails if there is no header in a SAM file. However, header is optional as specified in the...
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Forum: Bioinformatics
04-03-2015, 05:38 PM
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Replies: 7
Views: 10,113
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Forum: Bioinformatics
03-28-2015, 12:44 AM
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Replies: 3
Views: 1,500
I have read the documentation but still having...
I have read the documentation but still having problems. What I'm doing now is that, I'm simulating variants, mutations etc from a reference genome. I'd expect I'd see something from the GATK tool. I...
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Forum: Bioinformatics
03-26-2015, 04:21 PM
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Replies: 3
Views: 1,500
Protocol for finding variants in GATK
Hi,
I'm looking for a way to use GATK for finding variants. Unfortunately, their documentation is poor and misleading. The commands that they present on their presentation slides are out-of-dated....
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