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Search: Posts Made By: henry.wood
Forum: Bioinformatics 11-05-2018, 02:16 AM
Replies: 1
Views: 342
Posted By henry.wood
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...
Forum: General 06-09-2016, 01:37 AM
Replies: 2
Views: 1,011
Posted By henry.wood
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...
Forum: Illumina/Solexa 10-16-2015, 01:58 AM
Replies: 7
Views: 3,247
Posted By henry.wood
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...
Forum: Illumina/Solexa 02-02-2015, 08:11 AM
Replies: 5
Views: 934
Posted By henry.wood
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...
Forum: General 10-02-2014, 06:47 AM
Replies: 2
Views: 698
Posted By henry.wood
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...
Forum: General 10-01-2014, 05:41 AM
Replies: 2
Views: 698
Posted By henry.wood
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...
Forum: Illumina/Solexa 09-06-2013, 01:20 AM
Replies: 9
Views: 8,561
Posted By henry.wood
We switched to NEB library preps a few months ago...

We switched to NEB library preps a few months ago and are very pleased with them. They can produce good, libraries with no adapter peaks from samples which had previously failed with truseq due to...
Forum: Illumina/Solexa 06-19-2013, 02:06 AM
Replies: 7
Views: 3,247
Posted By henry.wood
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....
Forum: Sample Prep / Library Generation 05-02-2013, 01:45 AM
Replies: 3
Views: 2,443
Posted By henry.wood
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...
Forum: Illumina/Solexa 04-04-2013, 05:15 AM
Replies: 7
Views: 3,247
Posted By henry.wood
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...
Forum: Illumina/Solexa 03-05-2013, 04:23 AM
Replies: 20
Views: 6,254
Posted By henry.wood
I guess I'm a bit luckier than you with my sample...

I guess I'm a bit luckier than you with my sample sizes. Most of the FFPE samples have a fairly wide size range. The peak is around 100-200bp, but the tail often goes as high as 700bp. We prepare the...
Forum: Illumina/Solexa 03-01-2013, 01:43 AM
Replies: 20
Views: 6,254
Posted By henry.wood
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...
Forum: Bioinformatics 01-18-2013, 07:27 AM
Replies: 1
Views: 817
Posted By henry.wood
A quick way would be to do copy number analysis....

A quick way would be to do copy number analysis. I would recommend CNAnorm, mainly because I am one of the (minor) authors, but the wiki is full of others. You don't need to do a whole lane, just a...
Forum: Illumina/Solexa 11-01-2012, 03:22 AM
Replies: 20
Views: 6,254
Posted By henry.wood
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...
Forum: Illumina/Solexa 06-27-2012, 08:20 AM
Replies: 1
Views: 1,520
Posted By henry.wood
I was wondering the same recently. I happened to...

I was wondering the same recently. I happened to have a lane of mixed mouse and human samples, so aligned each library against the 'wrong' genome just to see what would happen. About 0.4% of the...
Forum: General 06-14-2012, 12:58 AM
Replies: 2
Views: 823
Posted By henry.wood
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...
Forum: Illumina/Solexa 05-30-2012, 05:22 AM
Replies: 6
Views: 51,249
Posted By henry.wood
Whenever we want to run a small number of samples...

Whenever we want to run a small number of samples on one lane, if we have enough DNA we make more than one library for each sample. If DNA is limited we do the steps up till tagging as normal, then...
Forum: Bioinformatics 03-19-2012, 03:04 AM
Replies: 12
Views: 3,733
Posted By henry.wood
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...
Forum: Bioinformatics 03-12-2012, 04:24 AM
Replies: 12
Views: 3,733
Posted By henry.wood
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...
Forum: Bioinformatics 02-27-2012, 05:47 AM
Replies: 1
Views: 1,184
Posted By henry.wood
You could use CNAnorm for the copy number part of...

You could use CNAnorm for the copy number part of your work. See http://seqanswers.com/forums/showthread.php?t=15618 for details. I should add the disclaimer that I am one of the authors. You should...
Forum: Bioinformatics 01-03-2012, 03:20 AM
Replies: 1
Views: 4,114
Posted By henry.wood
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...
Forum: General 12-21-2011, 08:35 AM
Replies: 9
Views: 3,043
Posted By henry.wood
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...
Forum: Sample Prep / Library Generation 12-09-2011, 02:20 AM
Replies: 7
Views: 3,346
Posted By henry.wood
I can't claim to be much of an expert, I was just...

I can't claim to be much of an expert, I was just passing on a paper that looked relevant. From my understanding the covaris doesn't over-shear too badly, so if you have the right settings, your...
Forum: Sample Prep / Library Generation 12-08-2011, 03:05 AM
Replies: 7
Views: 3,346
Posted By henry.wood
I don't have much experience doing this, but I...

I don't have much experience doing this, but I saw this paper http://www.ncbi.nlm.nih.gov/pubmed/22140562 which seems to address some of your concerns.
Forum: Sample Prep / Library Generation 11-07-2011, 01:24 AM
Replies: 5
Views: 3,562
Posted By henry.wood
Hmm, best ignore my covaris advice it seems. As...

Hmm, best ignore my covaris advice it seems. As for adaptors, I don't know what protocol or indeed machine you are working with. Just from an illumina point of view, since that's what we use - if...
Showing results 1 to 25 of 63

 


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