Adapter and quality trimming Mick Watson Director of ARK-Genomics The Roslin Institute

ADAPTER TRIMMING

Illumina technology Watch a video?

Illumina technology

Bridge Amplification

Key point: Sequence from Illumina may contain adapters

QUALITY TRIMMING

Quality trimming Take every read Remove bases at 5’ end (usually) or 3’ end (sometimes) that are below threshold Either remove after first bad base Or remove after average within sliding window falls below threshold

Paired-end and mate-pair 700bp 3000bp 2 x 100bp reads approx. 500bp apart 2 x 50bp reads approx. 3000bp apart A Paired-end B Mate-pair

Paired reads Paired reads represented by TWO fastq files Often named the same with _1.fastq, _2.fastq Or R1.fastq, R2.fastq Order of reads matters Read 1 in file 1 paired with read 1 in file 2 Etc

What happens if your quality trimmer removes read from one file but not the other?

Paired-end aware software? We will use sickle to trim on quality – It is paired-end aware We will use cutadapt to remove adapters – It is not paired-end aware