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Forum: Bioinformatics 10-18-2012, 11:48 AM
Replies: 10
Views: 2,742
Posted By bacdirector
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...
Forum: Bioinformatics 11-09-2010, 01:04 PM
Replies: 17
Views: 7,519
Posted By bacdirector
if you're using 50b reads, try trimming them to...

if you're using 50b reads, try trimming them to 35b in colorspace (i.e., use only the first 35 bases). Most of the -1's (no-calls) and sequencing errors occur between bases 36 and 50.

We've...
Forum: Bioinformatics 11-04-2010, 12:28 PM
Replies: 25
Views: 9,246
Posted By bacdirector
Ok, here it is - Percent of Reads that Map that Also Map Uniquely

In our study that started this thread, I originally reported a doubling of reads mapped from 25 million to 50 million achieved by trimming all reads >35 to 35. At 50b, we get only 25 million reads...
Forum: Bioinformatics 11-03-2010, 01:43 PM
Replies: 25
Views: 9,246
Posted By bacdirector
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...
Forum: Bioinformatics 11-02-2010, 12:23 PM
Replies: 25
Views: 9,246
Posted By bacdirector
50/52 million reads mapped....

50/52 million reads mapped....
Forum: Bioinformatics 11-02-2010, 12:22 PM
Replies: 25
Views: 9,246
Posted By bacdirector
@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...
Forum: Bioinformatics 11-02-2010, 12:16 PM
Replies: 25
Views: 9,246
Posted By bacdirector
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...
Forum: Bioinformatics 11-02-2010, 12:04 PM
Replies: 25
Views: 9,246
Posted By bacdirector
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....
Forum: Bioinformatics 11-02-2010, 11:47 AM
Replies: 25
Views: 9,246
Posted By bacdirector
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...
Forum: SOLiD 11-02-2010, 10:47 AM
Replies: 4
Views: 2,944
Posted By bacdirector
We doubled our mapping by trimming all reads > 35b to 35b

Please see thread in the Bioinformatics forum.

best,

jlw
Forum: Bioinformatics 11-02-2010, 10:42 AM
Replies: 25
Views: 9,246
Posted By bacdirector
Thumbs up 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...
Forum: Introductions 10-07-2009, 03:20 PM
Replies: 373
Views: 169,088
Posted By bacdirector
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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