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Search: Posts Made By: frc1230
Forum: Bioinformatics 05-22-2012, 08:19 AM
Replies: 9
Views: 2,192
Posted By frc1230
I like stampy-BWA, but it does take a lot of cpu...

I like stampy-BWA, but it does take a lot of cpu time
Forum: Bioinformatics 05-19-2012, 02:19 PM
Replies: 9
Views: 2,192
Posted By frc1230
I am currently trying to deal with exactly this...

I am currently trying to deal with exactly this problem: CASAVA alignments that choke mpileup. We use mpileup output directly for analysis with our own SNP finders, and it works very well with...
Forum: Illumina/Solexa 04-02-2012, 09:45 PM
Replies: 145
Views: 316,951
Posted By frc1230
I think in principle you are right, as far as I...

I think in principle you are right, as far as I know. I can't personally see any reason why it would be advantageous to switch the order of synthesis of the two arms, and without a compelling reason...
Forum: Illumina/Solexa 04-02-2012, 10:45 AM
Replies: 145
Views: 316,951
Posted By frc1230
As I understand it, the single-stranded sequences...

As I understand it, the single-stranded sequences in the Y-adapter must match the sequences immobilized on the chip. One must be identical to one of the chip sequences, and the other must be the...
Forum: Illumina/Solexa 10-14-2011, 07:45 AM
Replies: 10
Views: 3,856
Posted By frc1230
We're doing microbial genome re-sequencing, so we...

We're doing microbial genome re-sequencing, so we have the luxury of large amounts of material. The procedure turns out to be extremely sensitive to unknown contaminants in the initial DNA preps. ...
Forum: Illumina/Solexa 10-13-2011, 11:11 AM
Replies: 10
Views: 3,856
Posted By frc1230
Yes, I know those are included. But as it's set...

Yes, I know those are included. But as it's set up, as I understand it, you still don't know if something went wrong until the whole procedure is over (i.e. you're looking at the reads). At that...
Forum: Illumina/Solexa 10-13-2011, 07:14 AM
Replies: 10
Views: 3,856
Posted By frc1230
I'm aiming to put together a complete set of...

I'm aiming to put together a complete set of assays to test step-by-step how well the Illumina library prep works for any given sample. I have found the blind addition of reagents in a long sequence...
Forum: Illumina/Solexa 10-12-2011, 02:06 PM
Replies: 10
Views: 3,856
Posted By frc1230
We tested the ability of sonicated lambda-phage...

We tested the ability of sonicated lambda-phage DNA (from BRL, and sonicated with a Covaris instrument, or with a conventional tip sonicator) to self-ligate into concatemers, with or without prior...
Forum: Illumina/Solexa 09-28-2011, 04:58 PM
Replies: 145
Views: 316,951
Posted By frc1230
TruSeq sequence manipulations for library preparation

Kulukulas, thanks for the correction on the oligos.

The attached document contains my best guess as to how the new TruSeq kit works: by a similar principle as in my previous schematic, but there's...
Forum: Illumina/Solexa 07-07-2011, 07:49 AM
Replies: 145
Views: 316,951
Posted By frc1230
Illumina sequence manipulations

Hello, new to NGS, I've found this site extremely helpful. For my own edification and to help others in the same fog I was in, I put together a document with all the manipulations involved in...
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