Forum: Bioinformatics
10-18-2012, 10:48 AM
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Replies: 10
Views: 2,970
I'd recommend using % reads mapped and the # of...
I'd recommend using % reads mapped and the # of reads mapped uniquely as part of the evaluation, and keep in mind that the # of known heterozygotes is a measure of sensitivity, NOT accuracy. My two...
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Forum: Bioinformatics
11-09-2010, 12:04 PM
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Replies: 17
Views: 7,898
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Forum: Bioinformatics
11-04-2010, 11:28 AM
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Replies: 25
Views: 9,778
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Forum: Bioinformatics
11-03-2010, 12:43 PM
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Replies: 25
Views: 9,778
thanks, everyone
well, a lot of great feedback and perspective here; looks like a lot of people are doing different things; some use a masking tool, which should allow reads to map in spite of non-calls; that makes...
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Forum: Bioinformatics
11-02-2010, 11:23 AM
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Replies: 25
Views: 9,778
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Forum: Bioinformatics
11-02-2010, 11:22 AM
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Replies: 25
Views: 9,778
@brent
No this is total reads mapped. good point. As I said, we see an uptick in valid adjacent errors when we go lower than 30, but we see the lowest number of valid adjacent errors when we are between...
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Forum: Bioinformatics
11-02-2010, 11:16 AM
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Replies: 25
Views: 9,778
Thanks for the info on the blog.
Actually we...
Thanks for the info on the blog.
Actually we have found that the quality scores don't quite reflect the information that one would hope for SoLID - we found empirically that mapping is highest...
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Forum: Bioinformatics
11-02-2010, 11:04 AM
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Replies: 25
Views: 9,778
Actually, I'm surprised to hear that you think...
Actually, I'm surprised to hear that you think everyone knows about this... I've not seen anyone reference this approach in NGS studies that are published. Then again the 50bp kits were added late....
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Forum: Bioinformatics
11-02-2010, 10:47 AM
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Replies: 25
Views: 9,778
Nikloman,
In SoLiD, the reads were generated...
Nikloman,
In SoLiD, the reads were generated using the 50b read kit. The 'default' analysis to use all the reads in mapping, and to let mapping remove those with >1, 2, or 3 mismatches.
By...
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Forum: SOLiD
11-02-2010, 09:47 AM
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Replies: 4
Views: 3,063
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Forum: Bioinformatics
11-02-2010, 09:42 AM
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Replies: 25
Views: 9,778
Trimming SoLiD 50bp Reads = Doubling Our Mapping
We've all seen how the sequencing errors tend to found toward the 3' end of the read. We taken the task up of trimming reads for a highly over-covered study to 25, 30, 35... 50b. and mapping using...
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Forum: Introductions
10-07-2009, 02:20 PM
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Replies: 373
Views: 179,484
hello all
bioinformatics core director here with some questions, looking for advice
we have recently acquired the GS-FLX and the SoLiD. We are constructing a pricing model. Simple question: would you...
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