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Forum: Bioinformatics 10-10-2011, 01:02 AM
Replies: 6
Views: 8,699
Posted By maricu
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...
Forum: Bioinformatics 12-22-2010, 03:09 AM
Replies: 12
Views: 7,678
Posted By maricu
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
Forum: Bioinformatics 12-21-2010, 09:34 AM
Replies: 12
Views: 7,678
Posted By maricu
Unhappy 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......
Forum: Bioinformatics 11-19-2010, 07:28 AM
Replies: 3
Views: 5,823
Posted By maricu
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...
Forum: Bioinformatics 11-11-2010, 03:49 AM
Replies: 30
Views: 53,061
Posted By maricu
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...
Forum: Bioinformatics 11-03-2010, 11:37 PM
Replies: 2
Views: 3,102
Posted By maricu
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....
Forum: Bioinformatics 11-03-2010, 10:38 AM
Replies: 2
Views: 3,102
Posted By maricu
Question 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...
Forum: Bioinformatics 09-17-2010, 02:08 AM
Replies: 14
Views: 4,461
Posted By maricu
"The 1000 genomes projects found undetected indel...

"The 1000 genomes projects found undetected indel is the leading cause of false SNPs."
I arrived quite late to this thread but I'd like to know if there is a reference for such statement. Thanks
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