Forum: Bioinformatics
05-13-2014, 07:36 AM
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Replies: 2
Views: 2,032
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Forum: Bioinformatics
05-08-2014, 01:07 PM
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Replies: 2
Views: 2,032
Virmid - SNV mutation caller
Anyone here have any experience using Virmid? I have some exome seq data that I want to use it on but on first attempt with default parameters I get this error:
Exception in thread "main"...
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Forum: Bioinformatics
12-03-2012, 06:10 AM
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Replies: 5
Views: 2,965
Justin,
That is exactly what I wanted to...
Justin,
That is exactly what I wanted to know; mutate each codon and get the result. Thank you!
But I'm guessing 1:3.17 is not a biologically meaningful ratio because typically cancers (which is...
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Forum: Bioinformatics
11-28-2012, 07:52 AM
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Replies: 5
Views: 2,965
Query on NonSilent and Silent mutations..
What is the ratio of non-silent to silent mutations resulting from single nucleotide substitutions that can be expected, if every base is equally mutable and there is no selection pressure?
Hope...
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Forum: Bioinformatics
09-12-2012, 02:21 PM
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Replies: 5
Views: 1,705
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Forum: Bioinformatics
09-12-2012, 12:53 PM
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Replies: 5
Views: 1,705
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Forum: Bioinformatics
09-12-2012, 09:21 AM
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Replies: 5
Views: 1,705
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Forum: Bioinformatics
09-06-2012, 06:57 AM
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Replies: 2
Views: 1,548
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Forum: Bioinformatics
08-24-2012, 10:48 AM
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Replies: 2
Views: 1,548
Need help with CNV..
Hi,
I'm relatively new to bioinformatics. Have mastered SNVs and indels for the most part.. Now want to try my hand with CNVs.. I'm working with tumor-normal exome data..
My question is, is it...
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Forum: Bioinformatics
08-24-2012, 06:44 AM
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Replies: 5
Views: 1,932
I have a related question: Can the copy number...
I have a related question: Can the copy number algorithm of VarScan still be used if my tumor and normal data are sequenced to varying depths? Lets says mean tumor depth is 2.5 times mean normal...
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Forum: Bioinformatics
08-22-2012, 12:14 PM
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Replies: 34
Views: 10,273
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Forum: Bioinformatics
08-14-2012, 05:15 PM
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Replies: 7
Views: 2,266
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Forum: Bioinformatics
08-06-2012, 12:42 AM
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Replies: 7
Views: 2,266
It appears you have used MuTect to call your...
It appears you have used MuTect to call your SNVs. The current beta version of MuTect is very verbose and the initial output is more than a hundred fold bigger than it should be.
use "grep -v...
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Forum: Bioinformatics
08-03-2012, 01:13 AM
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Replies: 1
Views: 1,794
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Forum: Bioinformatics
07-31-2012, 11:07 AM
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Replies: 7
Views: 1,829
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Forum: Bioinformatics
07-30-2012, 02:45 PM
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Replies: 7
Views: 1,829
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Forum: Bioinformatics
07-30-2012, 10:08 AM
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Replies: 7
Views: 1,829
HI,
1) On IGV, they are not very different...
HI,
1) On IGV, they are not very different at the genomic level.. If I zoom in to look at finer details, the NimbleGen one has a lot of exons missing that are present in the refseq one (which is...
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Forum: Bioinformatics
07-30-2012, 10:04 AM
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Replies: 7
Views: 1,829
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Forum: Bioinformatics
07-27-2012, 04:01 PM
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Replies: 7
Views: 1,829
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Forum: Bioinformatics
07-26-2012, 04:04 PM
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Replies: 16
Views: 2,622
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Forum: Bioinformatics
07-26-2012, 02:16 PM
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Replies: 16
Views: 2,622
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Forum: Bioinformatics
07-25-2012, 07:37 PM
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Replies: 16
Views: 2,622
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Forum: Bioinformatics
07-25-2012, 06:37 PM
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Replies: 16
Views: 2,622
They are actually in standard UCSC refgene txt...
They are actually in standard UCSC refgene txt fomat. If you go to table browser, and try to export all fields in selected table as plain text, thats the kind of file. But the file that annovar uses...
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Forum: Bioinformatics
07-25-2012, 06:17 PM
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Replies: 16
Views: 2,622
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Forum: Bioinformatics
07-25-2012, 05:59 PM
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Replies: 16
Views: 2,622
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