Question: Find illumina adaptors
0
gravatar for sabaghianamir70
3 months ago by
iran
sabaghianamir7010 wrote:

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

ADD COMMENTlink modified 3 months ago by chen1.9k • written 3 months ago by sabaghianamir7010

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

ADD REPLYlink written 3 months ago by ATpoint22k

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

ADD REPLYlink modified 3 months ago • written 3 months ago by sabaghianamir7010
2

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.

ADD REPLYlink written 3 months ago by ATpoint22k
0
gravatar for genomax
3 months ago by
genomax71k
United States
genomax71k wrote:

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

ADD COMMENTlink written 3 months ago by genomax71k
0
gravatar for chen
3 months ago by
chen1.9k
OpenGene
chen1.9k wrote:

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.

ADD COMMENTlink written 3 months ago by chen1.9k
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