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Forum: Events / Conferences 07-12-2018, 06:08 PM
Replies: 0
Views: 830
Posted By najoshi
Variant Analysis, Bioinformatics Prerequisites, & Genome Browser workshops @ UC Davis

Announcing Three Upcoming Workshops at University of California, Davis (Davis, CA, USA)

UCSC Genome Browser Bioinformatics Prerequisites and Variant Analysis!

Each of these workshops is...
Forum: Academic/Non-Profit Jobs 11-20-2013, 03:01 PM
Replies: 0
Views: 1,059
Posted By najoshi
Unix System Administrator for the UC Davis Bioinformatics Core (Davis, CA)

The UC Davis Bioinformatics Core (http://bioinformatics.ucdavis.edu/) at the UC Davis Genome Center provides data analysis, infrastructure services, and training to the research community. We are...
Forum: Bioinformatics 10-01-2013, 06:54 PM
Replies: 0
Views: 2,201
Posted By najoshi
snpEff database provenance and custom builds

I am currently using snpEff to do effect prediction and I had a few questions. First, does someone have detailed information about the provenance of the data that was used to create the databases? ...
Forum: Bioinformatics 03-31-2011, 06:18 PM
Replies: 1
Views: 1,985
Posted By najoshi
samtools colorspace calmd is incredibly slow

Hi all,

I'm running samtools version 0.1.14 (and bwa version 0.5.8c) and I am
trying to do solid colorspace analysis on some single-end reads. I
indexed the reference using colorspace and I...
Forum: Bioinformatics 01-05-2011, 03:03 AM
Replies: 1
Views: 2,109
Posted By najoshi
Getting pileup to fastq with indels ala samtools.pl

Hi all,

So I need a program that will essentially do the functionality of samtools.pl pileup2fq, but I need it to take into account indels. It appears that pileup2fq only uses indels to determine...
Forum: Bioinformatics 04-09-2010, 04:40 PM
Replies: 1
Views: 2,040
Posted By najoshi
Problem running RepeatModeler (using WUBlast)

Hi all,

I am trying to run RepeatModeler on a fasta file that has about 415000 reads. What is strange is that the program runs through 4 rounds with no problem, but then in the 5th round I get...
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