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Search: Posts Made By: amcrisan
Forum: Bioinformatics 11-13-2013, 10:29 AM
Replies: 3
Views: 3,098
Posted By amcrisan
After some looking into this further and getting...

After some looking into this further and getting some suggestions and help from others, this is what I think the difficulty I had was.

The reason why the multi-sample vs. single sample variant...
Forum: Bioinformatics 11-06-2013, 11:28 AM
Replies: 3
Views: 3,098
Posted By amcrisan
Samtools multisample SNP caller

Hi -

I am running a comparison between running samtools SNP calling in the multi sample mode, vs using it on each file individually. I seem to be different getting per-sample genotypes when using...
Forum: Bioinformatics 11-13-2009, 11:20 AM
Replies: 7
Views: 3,420
Posted By amcrisan
As I understand it, the non-unique reads will not...

As I understand it, the non-unique reads will not necessarily be discarded. They will be placed asides and may be resolved at later steps using Mosaik sort (the -rmm option). If you don't choose to...
Forum: Bioinformatics 11-10-2009, 10:35 AM
Replies: 1
Views: 1,114
Posted By amcrisan
Mosaik Merge Error

Hello,

I've been trying to merge all of the sorted alignment files in a directory. According to the documentation this is possible. Each time I try do it I get the following error: ERROR: It seems...
Forum: Bioinformatics 11-10-2009, 10:24 AM
Replies: 7
Views: 3,420
Posted By amcrisan
That's difficult to say. The -m unique option...

That's difficult to say. The -m unique option will avoid giving you all the possible reads like the -m all option. However, all it does (according to the documentation) is really set aside any reads...
Forum: Bioinformatics 11-02-2009, 09:02 AM
Replies: 6
Views: 1,755
Posted By amcrisan
I am using Illumina..so no not colour space.

I am using Illumina..so no not colour space.
Forum: Bioinformatics 10-30-2009, 02:13 PM
Replies: 6
Views: 1,755
Posted By amcrisan
Mosaik assembly error

I get the following error when running Mosaik assembler... it starts of just fine, however after finishing up the chromosome 1 I get the following error:

- saving alignments from 10:
ERROR: An...
Forum: Bioinformatics 10-28-2009, 02:55 PM
Replies: 1
Views: 1,003
Posted By amcrisan
MOSAIK on transcriptome data

Has anyone attempted to use the Mosaik aligner on transcriptome data yet? Any thoughts?

Thanks.
Forum: Bioinformatics 10-23-2009, 10:16 AM
Replies: 1
Views: 2,658
Posted By amcrisan
mosaik jump database

Hello,

I am uncertain as how to make use of the mosaik jump database. I built my reference sequence as per the documentation, and when running the alignment I give it the following command:
...
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