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Forum: Bioinformatics 07-13-2011, 01:29 PM
Replies: 17
Views: 11,784
Posted By cow_girl
Ok I thought I had fixed the problem but its...

Ok I thought I had fixed the problem but its still not working!

When running a GATK tool I still get a read group error

##### ERROR MESSAGE: SAM/BAM file SAMFileReader{/586/586_merged.bam} is...
Forum: Bioinformatics 07-11-2011, 03:50 PM
Replies: 17
Views: 11,784
Posted By cow_girl
Just found the answer to my own question... it...

Just found the answer to my own question... it was right there under my nose in the documentation of course! I will post here in case anyone else encounters the same thing :)

A concrete example...
Forum: Bioinformatics 07-11-2011, 12:42 PM
Replies: 17
Views: 11,784
Posted By cow_girl
RG tags in merged BAM files, muliple lanes one sample

I know there are a few threads on this topic but I can't seem to find the answer to my particular problem!

I am merging BAM files from 8 lanes of sequencing, they are all the same sample, I want...
Forum: Bioinformatics 03-06-2011, 11:24 AM
Replies: 4
Views: 3,375
Posted By cow_girl
That worked perfectly, thank you! Now just to get...

That worked perfectly, thank you! Now just to get my SNP file correct :)
Forum: Bioinformatics 03-02-2011, 10:01 AM
Replies: 4
Views: 3,375
Posted By cow_girl
Input files for Roche GSMapper

I am using GSMapper to assemble 454 reads to a reference bovine genome.
I would like to specify a reference genome annotation and so that my variations can be easily identified as occurring in...
Forum: Bioinformatics 03-02-2011, 09:37 AM
Replies: 4
Views: 8,839
Posted By cow_girl
I also have been searching for a simple script or...

I also have been searching for a simple script or tool to convert to gff format to use in SNP annotation, I am wanting to convert xml to gff though. If you are working with the human genome you can...
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