お客さんに「どうやってペアドエンドのfastqからアダプター配列をトリミングするの？」と聞かれました。以下、TruSeqタイプについてのみですが、ご参考までに。
The question:
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For the adapter sequences, you gave me the following info:
AdapterRead1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
AdapterRead2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Are these from the 5’ or 3’ end? To which end of the sequence do you
attach the adapters? What is the difference between Read1 and Read2?
Do they go on different ends of the sequence?
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And here is my reply:
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I hope below will help!
http://bitesizebio.com/…/what-everyone-should-know-about-r…/
(the cartoon in the middle)
http://seqanswers.com/forums/archive/index.php/t-17521.html
(example cutadapt trimming scripts)
In case of paired end sequencing, trim Read1 adapter from Read1 fastq, and Read2 adapter from Read2 fastq.
