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Forum: Bioinformatics 07-07-2014, 09:37 AM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
sdmoore, By default, BBMap will look for...

sdmoore,

By default, BBMap will look for much longer indels than BWA/Bowtie2, over 16000bp. You can limit this with the maxindel flag (e.g. "maxindel=40"). Soft-clipping (via "local" flag) can...
Forum: Bioinformatics 07-06-2014, 08:25 PM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
sdmoore, BBMap does not have an option for...

sdmoore,

BBMap does not have an option for setting the readgroup, since I never encountered a situation where I needed it. But if it's useful, I can add it to the next release. The solution in...
Forum: Bioinformatics 06-27-2014, 03:26 PM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
Olaf, This has been fixed in the latest...

Olaf,

This has been fixed in the latest release, 33.04
Forum: Bioinformatics 06-23-2014, 06:02 PM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
Olaf, Currently, BBNorm uses single...

Olaf,

Currently, BBNorm uses single interleaved files for temporary storage when using multiple passes. And I have not implemented any way to specify dual files in intermediate stages, since...
Forum: Bioinformatics 06-23-2014, 03:44 PM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
Olaf, It's there, I just forgot to document...

Olaf,

It's there, I just forgot to document it; sorry! I'll add that to the shellscript in the next release. I think that all of the programs in the package that read fastq input allow the "qin"...
Forum: Bioinformatics 06-19-2014, 09:48 AM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
Sarah, It might be better to normalize using...

Sarah,

It might be better to normalize using a kmer length of 41, but BBNorm only supports a maximum of 31 :) In practice, it should make very little difference, though. Using long kmers is...
Forum: Bioinformatics 06-17-2014, 09:14 AM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
Sarah, Yes, BBNorm is the correct tool. ...

Sarah,

Yes, BBNorm is the correct tool.

I'm not sure, but I suspect that your shell is not bash. You could retry the command with "bash" instead of "sh", which may work. But the easier thing...
Forum: Bioinformatics 01-23-2014, 09:41 AM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
Thanks for the suggestion; I'll look into that!

Thanks for the suggestion; I'll look into that!
Forum: Bioinformatics 01-23-2014, 08:24 AM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
I have compared it to tophat, which it greatly...

I have compared it to tophat, which it greatly outperforms in speed and has higher sensitivity on real RNA-seq data. I have not yet compared it to STAR - I tried to but was unable to get STAR to run...
Forum: Bioinformatics 01-22-2014, 01:57 PM
Replies: 24
Views: 12,339
Posted By Brian Bushnell
BBMap - a new short read aligner, to be released soon.

BBMap will be publicly released soon, pending confirmation with LBL's legal department.

In the meantime feel free to look at these graphs of its performance:
...
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