Adapter and quality trimming

Mick WatsonDirector of ARK-Genomics

The Roslin Institute

ADAPTER TRIMMING

Illumina technology• Watch a video?

http://www.youtube.com/embed/45vNetkGspo

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