SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 6 of 6
Search took 0.00 seconds.
Search: Posts Made By: unagaswamy
Forum: Bioinformatics 11-11-2010, 06:55 AM
Replies: 9
Views: 9,806
Posted By unagaswamy
Hi Bruins, Thanks for this very useful link. It...

Hi Bruins,
Thanks for this very useful link. It definitely answers some of my questions.
-Uma
Forum: Bioinformatics 11-05-2010, 08:54 AM
Replies: 9
Views: 9,806
Posted By unagaswamy
Hi All, I generated a raw pileup for all...

Hi All,
I generated a raw pileup for all reference positions using the samtools. An exmaple record for a non-SNP position is below:
chrY 11936864 G G 51 0 60 8...
Forum: Bioinformatics 10-28-2010, 07:11 AM
Replies: 9
Views: 9,806
Posted By unagaswamy
Hi nilshomer, Thanks for the reply. We are...

Hi nilshomer,
Thanks for the reply. We are generating SAM record only for the SNP positions which does have the base quality. I am interested in the Non-SNP positions as well and hence I'm trying to...
Forum: Bioinformatics 10-25-2010, 10:03 AM
Replies: 9
Views: 9,806
Posted By unagaswamy
Hi Experts, Can anyone tell me how to extract...

Hi Experts,
Can anyone tell me how to extract the base quality from the CQ field of the BAM file? I colleague of mine mentioned that every two ASCII character corresponds to the SOLiD color space....
Forum: Bioinformatics 10-21-2010, 11:49 AM
Replies: 9
Views: 9,806
Posted By unagaswamy
Thanks for the info. Here is what I have tried...

Thanks for the info.
Here is what I have tried so far to view the file for a given sample:
samtools view filename.bam chr:start-end

For non SNP positions, I am getting the base coverage using...
Forum: Bioinformatics 10-20-2010, 07:15 AM
Replies: 9
Views: 9,806
Posted By unagaswamy
Question Extracting base coverage and quality values from BAM files

Experts,
I am interested in extracting base coverage and quality values for non SNP reads from a BAM file?
Thanks,
-Uma
Showing results 1 to 6 of 6

 


All times are GMT -8. The time now is 07:47 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO