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Search: Posts Made By: rworthi
Forum: Bioinformatics 12-01-2011, 06:56 PM
Replies: 4
Views: 2,227
Posted By rworthi
yes, I mean the Illumina OmniExpress Plus latest...

yes, I mean the Illumina OmniExpress Plus latest chip raw data. Are they even offering the exome product yet?
Forum: Bioinformatics 11-30-2011, 05:09 PM
Replies: 3
Views: 2,117
Posted By rworthi
this is a huge contribution! Thanks so much! ...

this is a huge contribution! Thanks so much!

I have been able to make it work in Debian, but not CentOS or Ubuntu, so this really helps.

Also, I have a VM image at bionimbus that works:
...
Forum: Bioinformatics 11-30-2011, 04:36 PM
Replies: 4
Views: 2,227
Posted By rworthi
23andme raw Illumina intensity reads

Has anyone been able to get the raw Illumina reads from 23andme?

I have asked repeatedly about this and just get a runaround answer. Are we not entitled to the raw data to do our own analysis,...
Forum: General 11-30-2011, 04:30 PM
Replies: 11
Views: 3,023
Posted By rworthi
I have 23andme and Nimblegen exome now, and...

I have 23andme and Nimblegen exome now, and Complete Genomics (or Amazon to be technical) is supposed to deliver WGS any minute. I am a PGP volunteer so it will all be public, but PGP still hasn't...
Forum: Bioinformatics 11-09-2011, 11:20 AM
Replies: 4
Views: 1,821
Posted By rworthi
Not that I know of, but they just started...

Not that I know of, but they just started offering bwa as an alternative mapping approach to their proprietary method.
Forum: Bioinformatics 10-27-2011, 11:26 AM
Replies: 3
Views: 2,117
Posted By rworthi
installing birdsuite

Has anyone been able to install the Broad's birdsuite on Ubuntu or CentOS?

I tried on Ubuntu 10.04 LTS 64-bit. First, the broadgap.* files would not install at step 5, and Broad support sent me...
Forum: Illumina/Solexa 09-28-2011, 12:25 PM
Replies: 4
Views: 10,285
Posted By rworthi
excellent! bow tie is purring away building the...

excellent! bow tie is purring away building the sam file. Thanks so much!

What splice mapper program(s) would you recommend, and is there anything I can use to recalibrate quality scores on these...
Forum: Illumina/Solexa 09-28-2011, 09:25 AM
Replies: 4
Views: 10,285
Posted By rworthi
thanks very much for all that great advice! The...

thanks very much for all that great advice! The read length is 90 bp. I made your modifications and shortened the read file names (and unzipped them) and now get this error, which I am sure is...
Forum: Illumina/Solexa 09-28-2011, 08:25 AM
Replies: 4
Views: 10,285
Posted By rworthi
bowtie command line for Illumina Hiseq 2000 with Illumina 1.5+ quality encoding files

I am trying to align some paired end exome reads with bowti, but despite using the bow tie -q" switch to recognize fast file, I keep getting the error:

./bowtie -q -n -r -S -t -p 2 -I 0 -X 100...
Forum: Bioinformatics 07-21-2011, 07:48 AM
Replies: 4
Views: 1,821
Posted By rworthi
assembling Nimblegen exome reads

I just got Nimblegen v2 exome data. I would like to assemble the reads, exon by exon. Is there a program that will do this? DNAnexus maps the reads to the Golden Path and provides variant calls, but...
Forum: Bioinformatics 06-30-2011, 04:05 PM
Replies: 0
Views: 1,400
Posted By rworthi
dbSNP build 133 & mysql

Does anyone know of a mysql table version of dbSNP build 133? I assume eventually it will appear at UCSC, but it may take a while.
Forum: Introductions 06-27-2011, 10:10 AM
Replies: 4
Views: 2,478
Posted By rworthi
SNPedia

Thanks for the tip. I use Promethease for my 23andme data, but I was not aware that they have incorporated CGI data analysis as well.
Forum: Bioinformatics 06-18-2011, 09:44 AM
Replies: 0
Views: 1,281
Posted By rworthi
human genome build identifier tool

Before I start working on this, does anyone have a tool that identifies which build a set of gene coordinates belongs to from among the human genome builds? I have run into several papers where the...
Forum: Introductions 06-18-2011, 09:38 AM
Replies: 4
Views: 2,478
Posted By rworthi
Complete Genomics user

I teach pharmacogenomics at Southern Illinois University and I am a subject of the Personal Genomes Project. I got a seed grant from my university an my genome is being sequenced by Complete...
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