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Adapter and quality trimming

Adapter and quality trimming. Mick Watson Director 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:.

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Adapter and quality trimming

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

  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

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