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Forum: Bioinformatics 06-24-2012, 09:12 AM
Replies: 18
Views: 11,899
Posted By JimC
Great ! that's what I was looking for !!

Great ! that's what I was looking for !!
Forum: Bioinformatics 06-24-2012, 06:22 AM
Replies: 18
Views: 11,899
Posted By JimC
MAPQ values in Tophat output

Can anyone address the MAPQ output from Tophat(1.4.1), where the accepted_hits.bam file, when viewed in sam format -- the MAPQ only values are 0, 1, 3, 255. I've looked through the whole file, and...
Forum: Bioinformatics 11-29-2011, 06:45 AM
Replies: 7
Views: 5,614
Posted By JimC
Odd behavior using samtools mpileup, bcftools

I've tried this a few times and I'm getting very occassional / odd behavior in the output from mpileup / bcftools / vcfutils varFilter. The output reports an indel, but upon examination of the...
Forum: Bioinformatics 11-29-2011, 06:04 AM
Replies: 9
Views: 2,890
Posted By JimC
Nils, I can't find any clear statement about...

Nils,
I can't find any clear statement about whether BWA or Bowtie handle IUPAC codes in reference sequences (or possible errors when using reference sequences with them included).

Can you...
Forum: Bioinformatics 05-11-2011, 10:27 AM
Replies: 10
Views: 3,011
Posted By JimC
Similar Problem

I have a similar problem and don't want to start a separate thread unless necessary.

Illumina HiSeq paired-end genomic DNA for Arabidopsis.
Reads aligned using BWA (aln and sampe modules)....
Forum: Bioinformatics 05-10-2011, 11:48 AM
Replies: 514
Views: 225,230
Posted By JimC
Try removing the command line option -a You are...

Try removing the command line option -a You are going to report ALL possible alignments for all reads. if you have repetitive sequences, this could be causing the memory problem. I would set a...
Forum: Bioinformatics 03-29-2010, 06:34 PM
Replies: 514
Views: 225,230
Posted By JimC
best-first chunk memory problem

Ben,
I've tried to read all the posts, but I may have missed this answer if posted.

I'm having problem with running bowtie on a mouse genome dataset.
The error is a large number of reads giving...
Forum: Bioinformatics 05-10-2009, 07:23 PM
Replies: 5
Views: 2,878
Posted By JimC
Mosaik Aligning with Solexa Reads

I've used Mosaik tools quite sucessfully in the past and I'm having an issue that I want to ask for help on....

I have _sequence.txt files which were sent to me from another lab for analysis, so...
Forum: Bioinformatics 11-16-2008, 08:25 AM
Replies: 1
Views: 2,470
Posted By JimC
Red face Analysis for Paired end reads

I've searched the forums at least a little bit and I'm not seeing any discussions on analysis of paired end reads. I'm having more and more bioinformatics requests for genome resequencing...
Forum: Introductions 11-11-2008, 07:27 AM
Replies: 0
Views: 1,914
Posted By JimC
Post Hello from Ann Arbor

I'm a bioinformatics analyst at the University of Michigan. I head up a nascent group which will be doing all sorts of bioinformatics projects including analysis of Next-Gen Sequencing and other...
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