Forum: Bioinformatics
10-10-2011, 01:02 AM
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Replies: 6
Views: 8,699
Hi all,
I noticed that BWA assigns mapping...
Hi all,
I noticed that BWA assigns mapping quality of 0 when it finds a "J" (or at least a bunch of them) in the quality string. So far I've opted for changing al J to I and then map with the...
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Forum: Bioinformatics
12-22-2010, 03:09 AM
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Replies: 12
Views: 7,678
Thanks Laura!!!
Yes indeed, I found the...
Thanks Laura!!!
Yes indeed, I found the vcftools, the sys admin will install soon and I will try it, but in the mean time I found a way to do it with awk, it works quite well!
M
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Forum: Bioinformatics
12-21-2010, 09:34 AM
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Replies: 12
Views: 7,678
Extracting genome specific SNPs from 1000 genomes
Hello!
I've been trying to get SNP data from the 1000 genome project, I've been looking at the vcf files, however I fail to understand if these report population,individual, or total variation......
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Forum: Bioinformatics
11-19-2010, 07:28 AM
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Replies: 3
Views: 5,823
BWA mapping fastq files with Illumina quality
Hello,
I am still new in these matters, I was told to map illumina reads to the human genome. I was given the fastq files and proceeded to use BWA, everything ran smoothly 'til today when I...
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Forum: Bioinformatics
11-11-2010, 03:49 AM
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Replies: 30
Views: 53,061
I might arrive quite late to this thread, but I...
I might arrive quite late to this thread, but I am going through the same dilemma... In one section of the 1000 genomes paper (suppl) they mention that they use rmdup and then to make sure the run...
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Forum: Bioinformatics
11-03-2010, 11:37 PM
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Replies: 2
Views: 3,102
Hi,
The program I want to use removes...
Hi,
The program I want to use removes clones an re calculates the quality string, I guess I can go back to sam once I know what reads are not clonal so I dont loose all the information....
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Forum: Bioinformatics
11-03-2010, 10:38 AM
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Replies: 2
Views: 3,102
sam/bam to bowtie
I have files in bam format of reads mapped with BWA, I would like to know if there's any tool available to convert to bowtie format. I have a program for downstream analysis (for the collapse of...
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Forum: Bioinformatics
09-17-2010, 02:08 AM
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Replies: 14
Views: 4,461
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