Find illumina adaptors
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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sabaghianamir70 •
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sabaghianamir70 •
2 answers
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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Which kit was used? That decides which adapter you have to look for.
thats what i dont know, how should i found out which kit used on my data ? i just saw the NEXTseq500
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
fastqcto check if there are adapter contaminations.fastqcrecognizes most common adapters.