Adapter and quality trimming
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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

Adapter and quality trimming

Mick Watson

Director of ARK-Genomics

The Roslin Institute


Adapter trimming

Adapter trimming


Illumina technology

Illumina technology

  • Watch a video?

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


Illumina technology1

Illumina technology


Bridge amplification

Bridge Amplification


Key point

Key point:

  • Sequence from Illumina may contain adapters


Quality trimming

Quality trimming


Quality trimming1

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

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


Paired reads

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


Adapter and quality trimming

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


Paired end aware software

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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