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Forum: Bioinformatics 07-25-2014, 12:49 AM
Replies: 6
Views: 2,732
Posted By shambo
Thanks Brian. I'll give it a shot and report back.

Thanks Brian. I'll give it a shot and report back.
Forum: Bioinformatics 07-24-2014, 05:38 AM
Replies: 6
Views: 2,732
Posted By shambo
I had this thought too. Looking at the bwa...

I had this thought too. Looking at the bwa command line, they specify the seed as -l 20bp with -k4 mismatches. I bumped up the number of mm to -k 5 (just to see) and not many more sites were found....
Forum: Bioinformatics 07-24-2014, 04:59 AM
Replies: 6
Views: 2,732
Posted By shambo
You're absolutely right, there is a 3 base PAM...

You're absolutely right, there is a 3 base PAM (NGG) on the end of the sequence. In my case all the sequences had the NGG when they were supplied to the mapper.

You are also right when you say the...
Forum: Bioinformatics 07-24-2014, 01:40 AM
Replies: 6
Views: 2,732
Posted By shambo
Finding CRISPR gRNA off-target matches using NGS mappers

Hi all,

To keep it brief I have about 3 million, 23bp sequences (gRNAs) which are putative CRIPSR-Cas9 sites, all of which I need to screened for off-target sites against the hg19 genome. I'm...
Forum: Academic/Non-Profit Jobs 06-24-2013, 04:46 AM
Replies: 0
Views: 1,989
Posted By shambo
Core bioinformatician- Lund University, Sweden

An opportunity for a Bioinformatician is available at the Biomedical Center (BMC) at Lund University Sweden, in a newly established bioinformatics core. The post holder will join a dynamic and...
Forum: Bioinformatics 05-02-2012, 08:37 AM
Replies: 0
Views: 2,009
Posted By shambo
Cuffdiff parameter regarding minimum reads within locus

Hi all,

I have two RNAseq samples which I've tophat'ed and have BAMS for. I'm trying out cuffdiff using a refseq GTF file.

The question is, if this param is set to 1000 for example, will it...
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