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Forum: Bioinformatics 06-20-2011, 03:41 AM
Replies: 3
Views: 1,641
Posted By mrxcm3
Srma

Hi,

Thanks for the reply - I figured this may the case. Here is the SAM. Thanks for taking a look.

@HD VN:1.0 GO:none SO:coordinate...
Forum: Bioinformatics 06-17-2011, 02:32 AM
Replies: 3
Views: 1,641
Posted By mrxcm3
SRMA - Error - cs TAG

Hi,

First time using SRMA, followed the user guide on source forge. Left all variables as defaults. It came up with this error. Any suggestions as to what I need to do to fix this?

...
Forum: Bioinformatics 03-24-2011, 02:44 PM
Replies: 5
Views: 6,999
Posted By mrxcm3
Whilst your specific problem is not one that I...

Whilst your specific problem is not one that I have had to consider - I have been working with anonomous (unbarcoded) sample pools. I have found these SNP callers useful;

SYZYGY
FREE BAYES...
Forum: Bioinformatics 01-12-2011, 09:21 AM
Replies: 3
Views: 2,495
Posted By mrxcm3
Softwear to visualise snps called from NGS

I used DeepSeq to identify novel SNPs in targeted amplicon regions. I have annotated these SNPs using variant classifier. However, I am yet to find a tool that can graphically display these SNPs in...
Forum: Bioinformatics 11-19-2010, 05:08 AM
Replies: 1
Views: 2,410
Posted By mrxcm3
Samtools version 1.0.7 and 1.0.10 different pileup

Hi

When I run pileup in samtools (samtools pileup -f ref.fa input.bam > results.pileup) I get considerably less reads when using v1.0.10 than 1.0.7. For example I have a 6kb amplicon - every base...
Forum: Bioinformatics 11-08-2010, 03:16 AM
Replies: 2
Views: 3,175
Posted By mrxcm3
Question Maq: Segmentation Fault

Hi

I am trying to map my SOLiD reads in Maq. I have converted my reads from .csfasta and .qual to .fastq using 'solid2fastq.pl'. I then generated a binary file using 'maq fastq2bfq'. I turned my...
Forum: Bioinformatics 11-03-2010, 09:25 AM
Replies: 3
Views: 5,217
Posted By mrxcm3
SNP calling software in pooled samples

I have some very deep seq data for a small genomic region (50kb) - generated in pooled samples using SOLiD - and I am looking to discover rare variants.

Can anyone recommend any good SNP callers...
Forum: Bioinformatics 10-31-2010, 10:05 AM
Replies: 2
Views: 3,523
Posted By mrxcm3
Thanks maubp this has worked :)

Thanks maubp this has worked :)
Forum: Bioinformatics 10-28-2010, 06:48 AM
Replies: 2
Views: 3,523
Posted By mrxcm3
Samtools 'import' and lost read group header

I am pretty new to manipulating NextGenSeq datasets, so my apologies if this question is trivial!

I want to format my .bam files so I can use them in GATK for SNP calling. Although my .bam files...
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