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Forum: Academic/Non-Profit Jobs 09-10-2017, 02:34 PM
Replies: 0
Views: 504
Posted By jdenvir
Assistant Professor faculty position, Marshall University, Huntington, WV USA

ASSISTANT PROFESSOR FACULTY POSITION: Biostatistics/Bioinformatics Faculty Position MARSHALL UNIVERSITY JOAN C. EDWARDS SCHOOL OF MEDICINE
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The Department of Biomedical Sciences in the Joan C....
Forum: Bioinformatics 05-19-2014, 01:04 PM
Replies: 0
Views: 1,870
Posted By jdenvir
GenomicFeatures: makeTranscriptDbFromUCSC suddenly started creating errors

I've been using the makeTranscriptDbFromUCSC function to retrieve ensembl genes from UCSC for over two years as part of our RNA-Seq expression profiling pipeline. Suddenly, last week, it started...
Forum: Academic/Non-Profit Jobs 03-12-2014, 01:20 PM
Replies: 0
Views: 1,104
Posted By jdenvir
Next Generation Sequencing Analyst, Marshall University, Huntington, WV USA

The Joan C. Edwards School of Medicine at Marshall University and WV- INBRE Program are seeking candidates for a full-time non-tenure-track position of Next Generation Sequencing (NGS) Analyst in the...
Forum: Bioinformatics 04-09-2013, 12:36 PM
Replies: 0
Views: 1,372
Posted By jdenvir
refGene.txt sizes and frameshifts of exons not consistent

I need to generate amino acid sequences and substitutions from genomic SNPs and reference genome sequences with gene annotations. Currently I'm doing this for mouse but will likely need to do this...
Forum: Bioinformatics 02-18-2013, 06:28 AM
Replies: 2
Views: 2,554
Posted By jdenvir
I ended up running Tophat2 over Bowtie 1; the...

I ended up running Tophat2 over Bowtie 1; the latest version of each resolved the problems I was having with crashing. It would be nice to understand why Bowtie2 is prohibitively slow, though.
Forum: Bioinformatics 10-26-2012, 10:28 AM
Replies: 2
Views: 2,554
Posted By jdenvir
Tophat2 very slow when running over Bowtie2

We recently completed our first RNA-seq runs on an Illumina Hi-Seq 1000. These were paired-end 100bp reads, with ~30-50 million paired reads per sample. Some are human cell line, some human patient...
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