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Search: Posts Made By: holmrenser
Forum: Bioinformatics 04-16-2015, 08:04 AM
Replies: 676
Views: 176,849
Posted By holmrenser
Hi Brian, I am trying to extract reads from...

Hi Brian,

I am trying to extract reads from a bbmap sam-file using picard SamToFastq and get an error about unpaired reads. Whether I tell BBmap to output paired only or not, picard SamToFastq...
Forum: Bioinformatics 03-17-2015, 09:44 AM
Replies: 2
Views: 1,115
Posted By holmrenser
Are you sure that you have a single gene that...

Are you sure that you have a single gene that spans >300Kb? Otherwise you have to include newlines in between genes.

This is directly from the glimmer manual...
Forum: Bioinformatics 03-17-2015, 09:40 AM
Replies: 8
Views: 2,830
Posted By holmrenser
We use bwa mem mostly, but I think we still use...

We use bwa mem mostly, but I think we still use bowtie2 for cufflinks/tophat/etc.
I recently started using BBMap and am impressed, although there is nothing to cite yet!
Forum: Introductions 12-07-2014, 11:44 PM
Replies: 2
Views: 885
Posted By holmrenser
Maybe you can provide us with a list of tools you...

Maybe you can provide us with a list of tools you tried and why they don't work, since you mentioned you have already tried some!
Forum: Bioinformatics 10-23-2014, 03:05 AM
Replies: 0
Views: 935
Posted By holmrenser
Repeatmodeler reproducibility

Dear all,

I am trying to identify repeats in a plant genome assembly using RepeatModeler. Currently my understanding is that RepeatModeler encompasses several repeat finding tools, some of which...
Forum: General 10-23-2014, 02:54 AM
Replies: 1
Views: 1,511
Posted By holmrenser
Hi, For annotating plant mitochondrial...

Hi,

For annotating plant mitochondrial genomes mitofy seems fine, what is it that you doubt about the results? If you want to gain insight into the repeats present in your mitochondrial genome I...
Forum: Bioinformatics 10-20-2014, 06:38 AM
Replies: 676
Views: 176,849
Posted By holmrenser
Hi Brian, I would be interested in knowing...

Hi Brian,

I would be interested in knowing when you intend to publish BBmap in a paper, can you enlighten us?

Cheers
Forum: Bioinformatics 07-31-2014, 06:42 AM
Replies: 6
Views: 1,240
Posted By holmrenser
First off: your grep will 'work', as in that it...

First off: your grep will 'work', as in that it will return some value.

Q1:
My guess would be that it is different because your grep only returns line numbers. So for a read containing the...
Forum: Bioinformatics 07-17-2013, 08:35 AM
Replies: 0
Views: 769
Posted By holmrenser
Extract node information from de Bruijn graph

I want to extract some specific properties of the nodes of the de Bruijn graph, following the methods of this publication: Wetzel et al.: Assessing the benefits of using mate-pairs to resolve repeats...
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