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Forum: Bioinformatics 03-20-2018, 10:07 AM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
Reformat won't do that, but you can use...

Reformat won't do that, but you can use partition.sh:

partition.sh in=X.fa out=X%.fa ways=10

That will produce 10 output files with an equal number of sequences and no duplication.
Forum: Bioinformatics 06-14-2016, 05:33 PM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
I just uploaded a new version of BBTools - 36.11...

I just uploaded a new version of BBTools - 36.11 - that supports idfilter (and subfilter, editfilter, etc) in Reformat. Bear in mind that reads mapped using old-style cigar strings ('M' symbol...
Forum: Bioinformatics 06-11-2016, 02:04 PM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
Not currently... I can add that, though. I'll...

Not currently... I can add that, though. I'll make a note to do that. BBMap has an "idfilter" flag, though.
Forum: Bioinformatics 03-23-2015, 01:03 PM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
Rod, You can now use the flags "addslash=t...

Rod,

You can now use the flags "addslash=t slashspace=f" together to accomplish that.

As an unrelated note, reformat now supports the "stoptag" flag, so it can process a sam file and add the...
Forum: Bioinformatics 03-17-2015, 04:36 PM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
Hi Rod, There is currently no way to fix...

Hi Rod,

There is currently no way to fix that. I specifically made it that way to replicate the name structure of real Illumina reads. For paired reads, many tools or formats (such as sam)...
Forum: Bioinformatics 02-24-2015, 12:31 PM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
Yep, that's the correct approach. The "reads=-1"...

Yep, that's the correct approach. The "reads=-1" flag is not necessary (that's the default), and "int=f" also gets forced automatically when you have dual input files.
Forum: Bioinformatics 01-27-2015, 10:14 AM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
Yes, it randomly subsamples. You can set the RNG...

Yes, it randomly subsamples. You can set the RNG seed with "sampleseed=NUMBER" if you want deterministic random sampling; by default, the seed is random.

Reformat can also give the first X reads...
Forum: Bioinformatics 10-13-2014, 08:38 AM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
This was caused by the bases and qualities having...

This was caused by the bases and qualities having different lengths. Either the fna and qual file do not go together, or their order is different, or one of the files is misformatted.

"reads.fna"...
Forum: Bioinformatics 08-28-2014, 09:35 AM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
No, the conversion from sam/bam is stateless and...

No, the conversion from sam/bam is stateless and 'dumb' - each line in the sam file will generate a FASTQ read, so secondary and chimeric alignments would cause problems.
Forum: Bioinformatics 08-27-2014, 11:37 AM
Replies: 39
Views: 33,342
Posted By Brian Bushnell
Introducing Reformat, a fast read format converter

Reformat (https://sourceforge.net/projects/bbmap/) is a member of the BBMap/BBTools package (http://seqanswers.com/forums/showthread.php?t=41057). It is a multipurpose tool designed for converting...
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