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Search: Posts Made By: gumbos
Forum: Bioinformatics 11-28-2012, 02:03 PM
Replies: 0
Views: 973
Posted By gumbos
Mining de-novo transcriptome assembly for transcripts missing in deletion mutant

I am hunting for transcripts missing in a mutant phenotype known to be a ~1mb genomic deletion. However, the genome assembly in this region is very poor. I have 4 lanes of RNAseq reads for both the...
Forum: Bioinformatics 06-23-2012, 03:21 PM
Replies: 5
Views: 2,840
Posted By gumbos
I am fairly sure I am using the correct reference...

I am fairly sure I am using the correct reference fasta because it was all done via a shell script. As a test, I went back and took chrM out of the fasta, and it worked. However, I am now stuck on...
Forum: Bioinformatics 06-22-2012, 03:39 PM
Replies: 5
Views: 2,840
Posted By gumbos
What more info can I provide? I am trying to run...

What more info can I provide? I am trying to run the GATK pipeline following the best practices page. I have generated a SAM using the newest bowtie2 beta. I convert that SAM to a BAM, sort it, index...
Forum: Bioinformatics 06-22-2012, 03:14 PM
Replies: 5
Views: 2,840
Posted By gumbos
GATK IndelRealigner error, badly formed genome loc: unknown contig chrM.

The original fasta file used to generate the alignments has the correct label of >ChrM. When I check the header of the input BAM I find the chrM @SQ line.

What could cause this?
Forum: Bioinformatics 06-08-2012, 09:58 AM
Replies: 12
Views: 10,202
Posted By gumbos
How did this go? I am looking into something to...

How did this go? I am looking into something to do allelic specific expression, specifically looking for nonsense mediated decay. Alleleseq looks promising. One problem is that I am working with...
Forum: Bioinformatics 01-09-2012, 09:01 AM
Replies: 1
Views: 4,856
Posted By gumbos
Targeted Genome Assembly for region poorly represented in reference genome?

Hello,

I am not sure if this is the best place to put this, but any help is appreciated.

I am working on identifying candidate genes for a mutation in a subtelomeric region of Zebrafish. The...
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