How to find out what adapters to remove after FastQC of RNAseq data?

Question

[ella]

Dear community,

For a new RNAseq project, I downloaded (foreign but reliable) SRA data of the wildtype control sampe. My FastQC analysis of the data reveals a significant "Illumina Universal Adapter" content, which I´d like to get rid of to have clean reads for later SNP calling analyses. In the FastQC/Configuration directory, I found the text file, that is used by FastQC to identify adapter sequences. The "Illumina Universal Adapter" sequence covers only 12bp.

For my own data's trimming and adapter removal (TruSeq3-PE.fa) I am using Trimmomatic.

Now my question: how do I know which adapters were used/ which adapter sequence I should trim for the downloaded WT SRA data?

Thanks a lot in advance,
Ella

Answer 1

[GenoMax]

You can use bbduk.sh from BBMap suite (How to figure out adapter sequence for Illumina reads? ) or fastp to figure out what potential adapter sequences are included.

That said if you are aligning to a good reference then you don't need to worry about adapters. Aligners should soft-clip (remove) any part of the read that does not align. Adapter sequences should not.

Note: No adapter sequence may be present or identifiable in good libraries which should have inserts longer than the length of sequencing. So there would be no adapter read through.

[ella]

Thank you for the fast help, I have the BBMap suite installed anyways and will try it out :)

[ella]

Worked nicely, thanks a lot :)