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Forum: Bioinformatics 07-21-2009, 12:09 PM
Replies: 10
Views: 3,027
Posted By dlepp
I'm having some strange issues with complementBed...

I'm having some strange issues with complementBed - it appears to be highly sensitive to convention used in the chromosome field. For example, this works:

Bed file:

chr21 32345 65443
...
Forum: Bioinformatics 04-17-2009, 08:17 AM
Replies: 13
Views: 16,725
Posted By dlepp
I wonder if you could explain the recalibration...

I wonder if you could explain the recalibration and point towards some tools?

Thanks.
Forum: Illumina/Solexa 04-15-2009, 02:21 PM
Replies: 6
Views: 12,938
Posted By dlepp
Illumina quality scores

I wonder if someone with more intimate knowledge of the Solexa pipeline could shed some light on the different varieties of quality scores produced and how they relate to one another. Just to be...
Forum: Bioinformatics 04-10-2009, 06:11 PM
Replies: 8
Views: 4,661
Posted By dlepp
Hi Dan, I was just to post on the very...

Hi Dan,

I was just to post on the very same problem. Most of my quality scores are "V"s, which converts to Q22 on the Illumina scale, if I have that correct (new to this). I'd be interested to...
Forum: Bioinformatics 03-30-2009, 08:35 PM
Replies: 5
Views: 5,378
Posted By dlepp
Velvet de novo assembly to amosvalidate

Also tried with no luck using .afg file produced from Solexa paired-end run. I was able to generate the bank and view it with Hawkeye, albeit painfully slowly, but ran into errors when running...
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