[Brian Bushnell]

Hmmm... no, not yet, though I did add into Clumpify's dereplication step the ability to count the number of duplicate reads and add "count=3", for example, to the name of a read representing 3 total reads (itself and 2 duplicates). It would not be difficult to modify that to report read identifiers. I'll add it to my todo list.

[darthsequencer]

Dear Brian,

I have been looking for a tool that would quickly dereplicate (100% containments) nucleotide sequences and track for each unique sequence the identifiers of the removed duplicates.

Something like:

dedupe.sh in=in.fa out=out.fa outd=outd.fa mid=100 mop=100

where:

in.fa:
seq1
seq2 (contained in seq1)
seq3 (contained in seq1)
seq4

out.fa:
seq1
seq4

outd.fa:
seq2
seq3

I am interested in:
seq1<tab>seq2,seq3
seq4

dedupe.sh does a fantastic job in returning out and outd, but I cannot find any option that would return the information I am interested in. Is this something that I am missing? Otherwise, I believe this could be a great feature, since compared to other tools that return this information, dedupe is so much faster.

Best,
Shini

Did anything like this get added to BBMap? Would be really helpful for me too!

[darthsequencer]

Ahh... sorry, but nope That would require reading the file twice, so it would not be easy to implement.

Oh yeah - duh

[Brian Bushnell]

Ahh... sorry, but nope That would require reading the file twice, so it would not be easy to implement.

[darthsequencer]

Actually, while it's not documented, the flag "minlength" also works with BBMap. Reads shorter than that will be discarded completely (they won't be output as unmapped).

Thanks for the tip - save me some space so I don't have to make additional files. I deal with a lot of libraries with different read lengths.

Is there a way to make BBMap require the smallest read to be some fraction of the longest read length? I know that's a niche use but BBMap always suprises me with it's built in functions.

[Brian Bushnell]

Actually, while it's not documented, the flag "minlength" also works with BBMap. Reads shorter than that will be discarded completely (they won't be output as unmapped).

[GenoMax]

You could pre-filter input data with

reformat.sh in=file.fq out=filt.fq minlength=N

[darthsequencer]

Hi Brian,
Is there a way to set a minimum input fragment length when mapping with BBMap?

[Brian Bushnell]

To do that, you'd need to trim all soft-clipped bases. I don't have any programs that will do so, but it looks like I could add it to Reformat without too much difficulty.

[jweger1988]

Hi Brian,

Is there anyway to use bbmap (or any other of your tools) to map a read to a reference file and then trim anything to the left of the reference sequence?

For example

My reference is
XXXXXXXXXXXXXXXXXX

And my reads are

NNNNXXXXXXXXXXXXXXXXXX
NNNXXXXXXXXXXXXXXXXXX
NNXXXXXXXXXXXXXXXXXX

I want them to be
XXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXX

I basically want to just trim anything of the left of the reads that doesn't match my reference? Thanks in advance.

[sdriscoll]

Oh yes! Thanks Brian.

[Brian Bushnell]

You can use the flag "intronlen" to control this. For example, "intronlen=100" will change the reporting so that all deletions of at least 100bp will reported using 'N' instead of 'D' in the cigar string.

[sdriscoll]

I was testing something with BBMap today and I realized I had forgotten something about how to use it and couldn't figure it out. I was mapping RNA-Seq and I thought that it would report spliced alignment cigars (using sam 1.3) as /[0-9]+M[0-9]+N[0-9]+M/ but it was reporting the introns as deletions with the [D] cigar value. Is that right or is there a way to get it to not do that?

Thanks-

[Brian Bushnell]

Hi Jweger,

Sorry, I don't have anything that will do that. Clumpify allows something sort of similar; you can create consensus sequence from raw reads, and map those. But that loses per-base depth information which is important for variant-calling, so I don't think it's what you want.

[jweger1988]

Hi Brian,

I'm wondering if there is any way you can get bbmap (or another of your tools) to give a consensus sequence of an alignment? I went to map to a ref sequence and then use that to create a consensus sequence and then use that to map again and then call variants.

Thanks!