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Find illumina adaptors
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10 months ago
iran

i have a data produce from nextseq 500 and i want to find the adapters which used in my data, how do i find that adapter in https://support.illumina.com/downloads/illumina-adapter-sequences-document-1000000002694.html

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Which kit was used? That decides which adapter you have to look for.

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thats what i dont know, how should i found out which kit used on my data ? i just saw the NEXTseq500

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That is the machine and does not tell you anything. Ask the people who made the data. Maybe one can make a best guess: What kind of data? RNA-seq, ChIP-seq? Try to run fastqc to check if there are adapter contaminations. fastqc recognizes most common adapters.

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10 months ago
chen ♦ 1.9k
OpenGene

Normally they are Illumina TruSeq adapters.

If you don't know it, use fastp to detect the adapters automatically.

See https://github.com/OpenGene/fastp#adapters for details.

Remind to enable --detect_adapter_for_pe option if your nextseq 500 data is paired-end.

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