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Forum: Bioinformatics 03-28-2016, 10:22 PM
Replies: 4
Views: 2,286
Posted By Alphabets
I want to call STRs with lobSTR dealing with the...

I want to call STRs with lobSTR dealing with the BAM file.

I run lobSTR with the paired-end BAM file (http://melissagymrek.com/lobstr-code/best-practices-wgs-wes.html#pairedbam) and it occurs many...
Forum: Bioinformatics 03-28-2016, 07:30 PM
Replies: 4
Views: 2,286
Posted By Alphabets
Thank you for your reply! I read your reply...

Thank you for your reply!

I read your reply carefully but there is some difficulty for me to understand.

Could you explain the three reads more easy to understand? or how can I solve the...
Forum: Bioinformatics 03-28-2016, 06:38 PM
Replies: 4
Views: 2,286
Posted By Alphabets
Three reads with the same name in the BAM file

Hi all,

I am dealing with the paired-end BAM file, and come up with many warnings like this:

WARNING: Could not find pair for HWI-ST430:177:2:1:4979:15503#0
WARNING: Could not find pair for...
Forum: Bioinformatics 03-21-2016, 04:53 PM
Replies: 7
Views: 1,627
Posted By Alphabets
The bam files I use are alignment of HiSeq reads...

The bam files I use are alignment of HiSeq reads aligned to the reference genome, removed redundancy and base realignments were done.

Does it matter? And how should I do?

Thank you!
Forum: Bioinformatics 03-21-2016, 04:56 AM
Replies: 7
Views: 1,627
Posted By Alphabets
Thank you for your reply. I agree with you, but...

Thank you for your reply. I agree with you, but there is something wrong with me.

When I run lobSTR with my name-sorted paired-end bam file just like what you mentioned, I get the follow...
Forum: Bioinformatics 03-20-2016, 05:06 PM
Replies: 7
Views: 1,627
Posted By Alphabets
I know what you mean, the --rg-sample and...

I know what you mean, the --rg-sample and --rg-lib parameters should not be the bam files. But I am confused of the third line "-f my_sample.bam --bampair". I think the -f parameter should be the...
Forum: Bioinformatics 03-20-2016, 01:12 AM
Replies: 7
Views: 1,627
Posted By Alphabets
lobSTR dealing with the paired-end BAM file

Hello:

I use the software lobSTR to deal with the paired-end bam file. As the document (http://melissagymrek.com/lobstr-code/best-practices-wgs-wes.html#pairedbam) shows, I should run the follow...
Showing results 1 to 7 of 7

 


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