Forum: Illumina/Solexa
01-20-2016, 06:17 AM
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Replies: 31
Views: 11,898
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Forum: Illumina/Solexa
01-19-2016, 01:39 PM
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Replies: 31
Views: 11,898
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Forum: Illumina/Solexa
01-11-2016, 04:42 PM
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Replies: 31
Views: 11,898
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Forum: Sample Prep / Library Generation
02-25-2014, 06:43 AM
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Replies: 11
Views: 6,186
From experience, it's totally okay to sequence...
From experience, it's totally okay to sequence these libraries. As ECO suggested, it's almost certainly adapter sequences annealing to each other. When you see this it usually means you did too many...
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Forum: Bioinformatics
07-25-2013, 07:33 AM
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Replies: 6
Views: 2,051
In general, your total coverage target should...
In general, your total coverage target should depend on your experimental setup. As the other posters have mentioned, if you're sequencing a 50mb genome, then all of your reads should come from that...
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Forum: Bioinformatics
06-20-2013, 08:52 AM
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Replies: 4
Views: 1,403
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Forum: Bioinformatics
06-20-2013, 08:41 AM
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Replies: 0
Views: 1,860
Predicting Cryptic Splice Sites?
Just wondering, would anyone be able to recommend software for predicting whether mutations will introduce cryptic splice sites into genes? I've come across several software packages that look like...
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Forum: Bioinformatics
06-17-2013, 09:41 AM
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Replies: 0
Views: 1,165
Is anyone using SNPSVM?
Hi, I just came across the paper on SNPSVM (http://bioinformatics.oxfordjournals.org/content/29/11/1361) in Bioinformatics. It was showing up as one of the most-read articles this month, and it seems...
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Forum: Bioinformatics
04-01-2013, 02:02 PM
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Replies: 6
Views: 2,234
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Forum: Bioinformatics
04-01-2013, 12:20 PM
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Replies: 6
Views: 2,234
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Forum: Bioinformatics
04-01-2013, 10:43 AM
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Replies: 6
Views: 2,234
Aligner that reports all alignments?
Hi, I'm looking for an aligner that reports multiple/all hits rather than just a single one. I know mrfast or BWA-short can do this for Illumina data, but is there any aligner that can do this that...
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Forum: Illumina/Solexa
11-19-2012, 09:02 AM
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Replies: 7
Views: 6,352
Capture or amplicon?
Hey all, I'm looking to sequence human exons across 189 genes totalling about 700kb. Is there anyone who's tried both target capture and amplicon sequencing who could tell me which would be better...
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Forum: Sample Prep / Library Generation
10-18-2012, 06:27 AM
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Replies: 7
Views: 2,831
Position-specific GC bias?
Hi, I've been having an unusual problem with my reads. I've been doing exome sequencing on a HiSeq 2000, but I'm getting only about 40% GC content at the start of each read, climbing to 45-50% closer...
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Forum: Bioinformatics
09-25-2012, 08:58 AM
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Replies: 2
Views: 1,173
Determining clinical significance of variants
Hi, I'm working with human exome samples. I'm hoping to pick out any mutations that have been previously reported as clinically significant, but I'm not sure which online databases or annotation...
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Forum: Bioinformatics
08-22-2012, 08:17 AM
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Replies: 15
Views: 10,891
Recalibration is applied to the entire BAM...
Recalibration is applied to the entire BAM equally. Here is an example.
GATK counts all examples of the sequence 'CG' in your BAM file with quality score 20 at read position 5, and it finds 1000...
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Forum: Bioinformatics
08-22-2012, 04:44 AM
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Replies: 15
Views: 10,891
Don't worry, you can do Base Quality Score...
Don't worry, you can do Base Quality Score Recalibration when you're searching for new mutations.
BQSR only counts mutations not in dbSNP as 'sequencing errors' for statistical purposes. It does...
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Forum: Sample Prep / Library Generation
08-21-2012, 09:53 AM
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Replies: 5
Views: 8,071
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Forum: Bioinformatics
08-20-2012, 06:48 AM
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Replies: 6
Views: 2,063
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Forum: Bioinformatics
08-01-2012, 06:22 AM
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Replies: 10
Views: 3,243
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Forum: Bioinformatics
08-01-2012, 05:54 AM
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Replies: 10
Views: 3,243
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Forum: Bioinformatics
08-01-2012, 04:57 AM
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Replies: 10
Views: 3,243
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Forum: Bioinformatics
08-01-2012, 04:48 AM
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Replies: 10
Views: 3,243
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Forum: Bioinformatics
07-23-2012, 09:11 AM
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Replies: 5
Views: 2,865
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Forum: Illumina/Solexa
06-29-2012, 10:08 AM
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Replies: 7
Views: 4,020
Interestingly, doing the capture with 1-2ug as...
Interestingly, doing the capture with 1-2ug as quantified by Qubit/Picogreen doesn't seem to adversely affect the capture at all, even though that sounds like it's ten times as much DNA as you'd use...
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Forum: Sample Prep / Library Generation
06-28-2012, 06:43 AM
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Replies: 21
Views: 9,923
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