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Search: Posts Made By: graveley
Forum: Bioinformatics 12-08-2010, 03:57 AM
Replies: 10
Views: 11,071
Posted By graveley
I had this same issue and discussed it with Cole...

I had this same issue and discussed it with Cole Trapnell. This issue arises because Cufflinks requires a tab delimited header in the SAM file you are using. Without the header, the GTF and SAM...
Forum: Illumina/Solexa 11-23-2009, 09:19 PM
Replies: 4
Views: 2,151
Posted By graveley
One of the perl scripts that comes with the...

One of the perl scripts that comes with the pipeline software can be used to generate splice junction indexes of any size you'd like.
Forum: Illumina/Solexa 11-23-2009, 09:07 PM
Replies: 9
Views: 84,342
Posted By graveley
We've done quite a bit of barcoding. Using a 3...

We've done quite a bit of barcoding. Using a 3 nt barcode, we've actually multiplexed up to 64 samples in a single lane. We have started using 6 nt barcodes which are composed of 2 repeats of a 3...
Forum: Bioinformatics 06-17-2009, 03:41 PM
Replies: 5
Views: 19,487
Posted By graveley
Hi, We are doing this routinely. We...

Hi,

We are doing this routinely. We typically use the -v 2 option and use an index made from both the genome and splice junctions with 69 nt on either side of the junction. Surprisingly, we get...
Forum: Academic/Non-Profit Jobs 06-04-2009, 07:39 PM
Replies: 0
Views: 1,647
Posted By graveley
Genomics Core Laboratory Director

Genomics Core Laboratory Director

The University of Connecticut Health Center (UCHC) Translational Genomics Core (TGC) is an active provider of microarray services to University and external...
Forum: Academic/Non-Profit Jobs 02-25-2009, 04:39 PM
Replies: 2
Views: 1,628
Posted By graveley
Hi Lee

Wow, how's it going. Wanna job? Would love to have you here. We should chat sometime. Email me when you get a chance.

Brent
Forum: Academic/Non-Profit Jobs 02-25-2009, 02:22 AM
Replies: 2
Views: 1,628
Posted By graveley
Genomics Core Laboratory Director

The University of Connecticut Health Center (UCHC) Translational Genomics Core (TGC) is an active provider of microarray services to University and external researchers, processing over 1,000...
Forum: Illumina/Solexa 01-24-2009, 10:39 AM
Replies: 3
Views: 3,474
Posted By graveley
Yes, as long as the sequences you use are the...

Yes, as long as the sequences you use are the same as the Illumina sequences, primers you synthesize yourself work fine!
Forum: Illumina/Solexa 01-24-2009, 10:37 AM
Replies: 12
Views: 3,931
Posted By graveley
Hi, my sales rep told me that version 3 of...

Hi,

my sales rep told me that version 3 of the sequencing kits are available for order starting Monday! Same pricing as v2 kits, but provide more accurate sequence so you can do 50-100 bp reads.
Forum: Illumina/Solexa 01-24-2009, 10:33 AM
Replies: 145
Views: 296,471
Posted By graveley
Hi, I run the site you got the sequences...

Hi,

I run the site you got the sequences from and am happy to see that you have posted the info here as well. I will attempt to keep the list up to date as new sequences are released. If there...
Forum: Bioinformatics 01-24-2009, 10:23 AM
Replies: 57
Views: 34,732
Posted By graveley
Dear Yogesh, We do this by writing a perl...

Dear Yogesh,

We do this by writing a perl script that reads in the alignment information and writes a new file in the appropriate format. I would send you what we use, but we do not use...
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