How can I get Adapter information for SRR File from SRA ?

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5.2 years ago

akshay_ware ▴ 30

Hi,

I am doing RNA-Seq analysis on sequencing data from SRA. I want to remove the adapters from the file. how can i get to know, what adapter sequences they used while sequencing? Or how can I trimmed this adapters?

Thank you

RNA-Seq Assembly sequencing next-gen alignment • 1.5k views

ADD COMMENT • link 5.2 years ago by akshay_ware ▴ 30

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Check with fastqc if adapters can be detected. If not there is probably nothing to worry about towards trimming, so not necessary. Scan the method section for the kit they used which determines the adapter.

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

ADD REPLY • link 5.2 years ago by ATpoint 86k

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See: A: How to get adapter information from SRA dump FASTQ file??

ADD REPLY • link 5.2 years ago by GenoMax 148k

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Also if the adapter content is less than 1% you can simply ignore it, since aligner like BWA softclips the adapters from ends when they dont align during alignment step.

ADD REPLY • link 5.2 years ago by rohitsatyam102 ▴ 920

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