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Forum: Bioinformatics 11-18-2011, 06:54 AM
Replies: 8
Views: 2,931
Posted By M&M
Thanks Simon! I found this script handy as well.

Thanks Simon! I found this script handy as well.
Forum: Bioinformatics 09-02-2011, 09:19 AM
Replies: 1
Views: 2,139
Posted By M&M
vcf snp genotype

I made snp calls on a set of 14 samples with samtools mpileup.

How do I determine the genotype call in a particular sample from the vcf file?

An example entry (some fields omitted for...
Forum: RNA Sequencing 08-26-2011, 05:41 AM
Replies: 0
Views: 1,393
Posted By M&M
Calculate baseline expected fpkm?

Is there a measure I could use to calculate a baseline expected fpkm per transcript based on sequencing coverage in a single sample? I'd then like to use this to compare with the fpkm generated from...
Forum: Bioinformatics 08-11-2011, 02:02 PM
Replies: 7
Views: 3,930
Posted By M&M
I was using the pre-compiled linux binary....

I was using the pre-compiled linux binary. Another member of our group had no problems generating fusion files with human RNA data from the same install. I run the standard flavor of Tophat just fine...
Forum: Bioinformatics 08-10-2011, 12:48 PM
Replies: 7
Views: 3,930
Posted By M&M
Tophat Fusion error with mRNAseq data

I tried to run TopHat Fusion on canine mRNA-seq data (Illumina paired-end), but received the error below.

Perhaps it is an inappropriate use of the software (giving it RNA data instead of DNA...
Forum: Bioinformatics 08-07-2011, 12:13 PM
Replies: 1
Views: 1,489
Posted By M&M
Did you ever find a resource to do this? I would...

Did you ever find a resource to do this? I would be interested in the same type of thing.
Forum: RNA Sequencing 08-01-2011, 03:00 PM
Replies: 0
Views: 1,565
Posted By M&M
Forum: Bioinformatics 07-29-2011, 05:33 AM
Replies: 14
Views: 7,047
Posted By M&M
Two ways around it

1. Check out Screen. I recommend this because it is easier to keep your jobs organized if you lots of jobs from different programs. I like to open separate 'screens' for each program, and name the...
Forum: Bioinformatics 07-08-2011, 07:43 AM
Replies: 14
Views: 7,047
Posted By M&M
Plattsa described the source of my error exactly....

Plattsa described the source of my error exactly. I found this thread helpful to correct the problem.

http://seqanswers.com/forums/showthread.php?t=12039

Lesson learned: always check for...
Forum: Introductions 06-27-2011, 09:52 AM
Replies: 0
Views: 1,048
Posted By M&M
Graduate Student venturing into NGS

I'm a graduate student getting into translational research at Van Andel Research Institute in Grand Rapids, MI. Sequencing will be a big part of what we're trying to do, and I have a huge set of...
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