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Search: Posts Made By: James W. MacDonald
Forum: Bioinformatics 01-05-2011, 07:15 AM
Replies: 2
Views: 1,593
Posted By James W. MacDonald
That was my first thought. And yes, I do. I am...

That was my first thought. And yes, I do. I am actually running other instances of bfast match right now, without problems. It's just this SOLiD run that is giving me problems.
Forum: Bioinformatics 01-05-2011, 06:19 AM
Replies: 2
Views: 1,593
Posted By James W. MacDonald
Error during Bfast match step

I get the following error when running the match step of bfast:

Searching index file 10/10 (index #10, bin #1)...
Reading index from...
Forum: Bioinformatics 12-20-2010, 08:08 AM
Replies: 2
Views: 2,040
Posted By James W. MacDonald
Retracted. Never mind.

Retracted. Never mind.
Forum: Bioinformatics 12-17-2010, 07:48 PM
Replies: 2
Views: 2,040
Posted By James W. MacDonald
Pipe and filter model with bfast+bwa 0.6.4e

Is it no longer possible to use the pipe and filter model with this version of bfast? If I pipe from bfast match to bfast localalign, I get a complaint that I am missing a -O and -T. Adding an -m -...
Forum: Illumina/Solexa 11-11-2008, 09:14 AM
Replies: 6
Views: 2,869
Posted By James W. MacDonald
You can use Bioconductor tools to find and...

You can use Bioconductor tools to find and eliminate the linkers. See the example here:

http://bioconductor.org/packages/2.3/bioc/vignettes/Biostrings/inst/doc/Alignments.pdf

The adapter...
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