Question

How to find adaptor sequences from SRA sample?

0

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4.5 years ago

akshay_ware ▴ 30

Hi,

I am doing small RNA sequencing data analysis from SRA database. I want to know which are the adapter sequences are present in that samples. how do I get that?

Thank You

RNA-Seq alignment sequencing next-gen rna-seq • 1.3k views

ADD COMMENT • link updated 4.5 years ago by h.mon 35k • written 4.5 years ago by akshay_ware ▴ 30

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Please use the search function, this has been asked many times before. Check also the column on the right-hand side of this post, there are suggestions for previous posts on the same topic.

How Can I Tell What Is The Adapter Used In A Sequence Read Archive (Sra) Sample?

How do I find out the adaptor sequences for SRA data?

Illumina Adapters for Small RNA seq

Also, you should read the method section to find out which kit was used, and then simply google for adapter sequence small rna <name of the kit>. Odds a good that it is the standard smallRNA adapter for Illumina.

ADD REPLY • link 4.5 years ago by ATpoint 81k

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what have you tried so far? This is not a very difficult question.

FastQC?

ADD REPLY • link 4.5 years ago by lieven.sterck 15k

score 3 · Accepted Answer · 2019-10-14

This question is a FAQ, it has been asked since the early days of BioStars to this day. For example, these questions are less than one week old:

Determine adapter sequence in RNA-seq samples

How can I get Adapter information for SRR File from SRA ? (by the way, please do not post duplicate / very similar questions)

As I said in C: Determine adapter sequence in RNA-seq samples , fastp can auto-detect adapters for both single-end and paired-end samples, so it is a good bet if you know nothing about the adapters.