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

2. ADAPTER TRIMMING

3. Illumina technology Watch a video? http://www.youtube.com/embed/45vNetkGspo

4. Illumina technology

5. Bridge Amplification

6. Key point: Sequence from Illumina may contain adapters

7. QUALITY TRIMMING

8. 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

9. 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

10. 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

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

12. 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