How to remove Illumina Small RNA 3' Adapter?

Question

[LDT]

I have downloaded a dataset which gives me an exciting time. I am trying with Trimmomatic to remove the adapters, but I have had no luck.

Whatever I am trying the adapters will not be removed

When I check with fastqc these are the overrepresented sequences, but it does not help me. Has anyone had a similar problem, and how did you solve it?

Answer 1

[GenoMax]

bbduk.sh has Illumina small RNA adapter in adapters.fa file included in resources directory of BBTools package. You can do something like the following:

bbduk.sh -Xmx4g in=fastq.gz out=trimmed.fastq.gz k=7 ktrim=r minlen=10 ref=/path/to/adapters.fa

A guide is available: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/

[LDT]

Thank you, GenoMax

[GenoMax]

adapters.fa is in a folder called "resources" in software you downloaded. You can simply copy it to an easy location in your $PATH.