Trimmomatic is another that I regularly use. It works with both single and paired-end reads.
Trim adapter sequence for single-end
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.
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EagleEye
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dianalves17 •
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dianalves17 •
2 answers
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.
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Brian Bushnell
Yes, if the FASTQC shows adaptor sequence is present in your file.
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