SRA toolkit (NCBI) - sra to fasta

Question

[t.kranenburg]

Dear all,

At the moment I'm trying to download sequences from the Sequence Read Archive (SRA) from NCBI and put them into fasta format. For this I downloaded the SRA-toolkit of NCBI and used the following code:

set PATH=%PATH%;C:\Users\Admin\Desktop\sratoolkit.2.9.0-win64\sratoolkit.2.9.0-win64\bin
prefetch --max-size 100000000 SRR390728
fastq-dump C:/Users/Admin/ncbi/public/sra/SRR390728.sra

(The SRA SRR390728 is the example SRA of the toolkit, since it is relatively small in size).

The SRA is downloaded as .sra. I was wondering what I should do to turn this .sra into .fasta?

Kind regards

[ATpoint]

You're lucky, the file is open access and available in fastq format from ENA.

Answer 1

[sangram_keshari]

You can use the same utility fastq-dump from SRA toolkit to convert from .SAR to either .fastq or .fasta.

fastq-dump --split-files --fasta 60 SRR390728

This above command will produce two (--split-files) fasta files (--fasta) with 60 bases per line ("60" included after --fasta)

For more details - fastq-dump function help from SRA toolkit

[t.kranenburg]

Thanks a lot. That helped

[Sanjukta]

Hi there, will it be an issue if we do not mention 60?

[ATpoint]

Can be 23 or 109, it does not matter.