Find illumina adaptors

Question

[sabaghianamir70]

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

[ATpoint]

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

[sabaghianamir70]

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

[ATpoint]

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.

Answer 1

[GenoMax]

A: Identify adapter sequences for trimming from Illumina paired end fastq files

Answer 2

[chen]

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.