Question: SRA toolkit (NCBI) - sra to fasta
0
gravatar for t.kranenburg
11 months ago by
t.kranenburg40
t.kranenburg40 wrote:

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,

sri sequence toolkit fasta ncbi • 888 views
ADD COMMENTlink modified 11 months ago by sangram_keshari130 • written 11 months ago by t.kranenburg40
1

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

ADD REPLYlink written 11 months ago by ATpoint15k
2
gravatar for sangram_keshari
11 months ago by
sangram_keshari130 wrote:

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

ADD COMMENTlink modified 11 months ago • written 11 months ago by sangram_keshari130

Thanks a lot. That helped

ADD REPLYlink written 10 months ago by t.kranenburg40
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