How to find out what adapters to remove after FastQC of RNAseq data?
1
0
Entering edit mode
12 months ago
ella • 0

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

Trimmomatic FastQC NGS RNA-seq • 860 views
ADD COMMENT
1
Entering edit mode
12 months ago
GenoMax 146k

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Worked nicely, thanks a lot :)

ADD REPLY

Login before adding your answer.

Traffic: 2009 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6