Trim adapter sequence for single-end

Question

[dianalves17]

Hey,

I want to do gene expression analysis from single end reads using RNA-Seq data produced by Illumina 2500. According to FastQC report some of the over-represented correspond to Illumina adapter sequences. Should I remove adapter sequences before alignment with Tophat?

Thank you.

Answer 1

[Brian Bushnell]

Yes, you should. I recommend this procedure for single-ended reads, using the BBMap package:

bbduk.sh in=reads.fq out=trimmed.fq ref=adapters.fa k=23 hdist=1 mink=11

"adapters.fa" is distributed with BBMap.

[Ian]

Trimmomatic is another that I regularly use. It works with both single and paired-end reads.

Answer 2

[EagleEye]

Yes, if the FASTQC shows adaptor sequence is present in your file.

http://cutadapt.readthedocs.io/en/stable/guide.html