bbduk.sh trimming to BAM output file

Question

[bge]

Hi,

I want to use bbduk.sh to trim reads in a uBAM file and write the trimmed reads to a new uBAM file. It appears that the reads in the output file are not trimmed.

One set of bbduk.sh parameters that I tried is

literal=polyA k=12 mink=11 ktrim=r trimclip=t

I see trimmed reads when the output file format is fastq but not when BAM or SAM.

Perhaps I am missing something?

Thank you!

Brent

Answer 1

[GenoMax]

Using a uBAM input and writing uBAM output is indeed not working directly. Probably because it is an edge case that @Brian likely did not test/code for.

Following seems to work for me for a single-end read file. Convert uBAM to fastq | trim using bbduk | write the result out as uBAM.

$ reformat.sh -Xmx3g in=test.bam out=stdout.fq int=f | bbduk.sh -Xmx3g in=stdin.fq out=stdout.fq int=f forcetrimleft=10 | reformat.sh -Xmx3g in=stdin.fq out=trimmed.bam int=f

[bge]

Hi,

I appreciate the confirmation -- I worry that I mess up.

Anyway, the input uBAM file has a tag with the barcode+umi sequences required by STARsolo. I don't see a straightforward way to preserve this information with a conversion to fastq.

Do you know whether this program is maintained?

Thank you!

Brent

[GenoMax]

BBMap is actively maintained but what you have is an edge case. You can try writing to Brian Bushnell (his email can be found in software in-line help).

Why do you need to trim the data? STARsolo may be able to handle it as is.