Forum: Bioinformatics
11-05-2018, 01:16 AM
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Replies: 1
Views: 1,067
I had a problem like this a while back. If your...
I had a problem like this a while back. If your tiled amplicons can be identified and separated form their start-end positions, you can split them into separate bam files. Varscan2 has the option of...
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Forum: General
06-09-2016, 12:37 AM
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Replies: 2
Views: 1,722
Have you looked at the distribution of read...
Have you looked at the distribution of read lengths in the badly behaved sample. I was having this issue a while back and found that many more reads in poor samples were the wrong length. If I'm...
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Forum: Illumina/Solexa
10-16-2015, 12:58 AM
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Replies: 7
Views: 4,300
I don't know if you're asking me or mmah. We...
I don't know if you're asking me or mmah. We think the problem was that our libraries were not being quantified correctly, and their concentrations were underestimated. For some reason Haloplex...
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Forum: Illumina/Solexa
02-02-2015, 07:11 AM
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Replies: 5
Views: 1,635
I think the high number of alternate reference...
I think the high number of alternate reference loci is a fairly plausible explanation. Looking at all the alternatives, for chr19, in total, they add up to about a quarter of the length of the...
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Forum: General
10-02-2014, 05:47 AM
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Replies: 2
Views: 1,140
Thanks for answering so quickly.
We aren't...
Thanks for answering so quickly.
We aren't targeting the same journals at the moment. Even if we were, the odds of getting all papers in their first choice journal is not great. (Sadly I do not have...
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Forum: General
10-01-2014, 04:41 AM
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Replies: 2
Views: 1,140
My papers all need to cite each other
I was wondering if I could query the collective experience. I am working on a number of projects, and their papers all need to cite data from the other projects as controls, but I'm worried that will...
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Forum: Illumina/Solexa
09-06-2013, 12:20 AM
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Replies: 9
Views: 10,865
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Forum: Illumina/Solexa
06-19-2013, 01:06 AM
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Replies: 7
Views: 4,300
We've made improvements, but they're not...
We've made improvements, but they're not completely solved. Our first go for the troublesome samples was loading 10pM and we got around 10% of reads passing filters with cluster density > 1000K/mm2....
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Forum: Sample Prep / Library Generation
05-02-2013, 12:45 AM
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Replies: 3
Views: 3,240
My bams had something, but not as much as they...
My bams had something, but not as much as they should. I asked a question about this a few weeks ago but got no response. We sequenced two lanes on a HiSeq and they were fine, but a third and fourth...
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Forum: Illumina/Solexa
04-04-2013, 04:15 AM
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Replies: 7
Views: 4,300
Very low read numbers from haloplex libraries
Hello all. We've recently done some HiSeq sequencing of pooled haloplex libraries. We have sequenced 6 lanes so far from 4 different captures. 4 of those lanes have behaved themselves perfectly, but...
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Forum: Illumina/Solexa
03-05-2013, 03:23 AM
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Replies: 20
Views: 8,140
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Forum: Illumina/Solexa
03-01-2013, 12:43 AM
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Replies: 20
Views: 8,140
I'd forgotten I said I'd report back. Oops. So...
I'd forgotten I said I'd report back. Oops. So the libraries worked OK. The DNA was reasonably good quality for FFPE, so degraded a bit, but still possible to do 500bp PCRs. It was proper surgical...
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Forum: Bioinformatics
01-18-2013, 06:27 AM
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Replies: 1
Views: 1,363
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Forum: Illumina/Solexa
11-01-2012, 02:22 AM
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Replies: 20
Views: 8,140
We are currently awaiting the results of FFPE...
We are currently awaiting the results of FFPE exomes. We used the illumina nextera exome kits. They worked with <100ng DNA from FFPE samples. The libraries looked fine, but we won't know how the data...
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Forum: Illumina/Solexa
06-27-2012, 07:20 AM
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Replies: 1
Views: 2,227
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Forum: General
06-13-2012, 11:58 PM
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Replies: 2
Views: 1,288
I guess it depends what you have access to. We...
I guess it depends what you have access to. We have a GAII. 6 samples (human?) tagged together on one lane would give between 3-4 million reads per sample, so a read every 1Kb or so. You would get...
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Forum: Illumina/Solexa
05-30-2012, 04:22 AM
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Replies: 6
Views: 52,518
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Forum: Bioinformatics
03-19-2012, 02:04 AM
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Replies: 12
Views: 5,224
You're right. It's a while since I did it and...
You're right. It's a while since I did it and I've forgotten the details. I didn't use all the reads, I only used the reads were there wasn't perfect alignment. So I kept the reads where one pair...
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Forum: Bioinformatics
03-12-2012, 03:24 AM
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Replies: 12
Views: 5,224
One thing I was playing around with a little...
One thing I was playing around with a little while back was to try and assemble the predicted breakpoints. I took all the reads in which either pair mapped near the breakpoint and put them into...
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Forum: Bioinformatics
02-27-2012, 04:47 AM
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Replies: 1
Views: 1,784
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Forum: Bioinformatics
01-03-2012, 02:20 AM
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Replies: 1
Views: 5,630
It's due to a difference in the library prep....
It's due to a difference in the library prep. Directional RNA-seq keeps the strand information by only making the cDNA in one direction, non-directional will make cDNA in both directions, so you have...
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Forum: General
12-21-2011, 07:35 AM
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Replies: 8
Views: 4,429
I'm an author on a paper which is coming out...
I'm an author on a paper which is coming out sometime in January where we have looked for HPV sequence in cancer genomes. You don't need that many reads to detect the virus. 1 million reads per...
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Forum: Sample Prep / Library Generation
12-09-2011, 01:20 AM
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Replies: 7
Views: 4,679
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Forum: Sample Prep / Library Generation
12-08-2011, 02:05 AM
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Replies: 7
Views: 4,679
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Forum: Sample Prep / Library Generation
11-07-2011, 12:24 AM
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Replies: 5
Views: 4,684
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