Question: converting the format of read files in GEO datasets (SRA) to fasta and fatsq
2
gravatar for A
5.1 years ago by
A3.8k
A3.8k wrote:

Hey guys,

I have an accession number, how i can convert the sra to fasta in windows??

 

 

rna-seq • 2.8k views
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by A3.8k
3
gravatar for arnstrm
5.1 years ago by
arnstrm1.8k
Ames, IA
arnstrm1.8k wrote:

You can use SRAtools for this purpose. I think it is available for both Windows and Linux. Once installed, you can download/convert sra files to fastq as follows:

fastq-dump myfile.sra #for single end
fastq-dump --split-files myfile.sra #if paired end

 


 

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by arnstrm1.8k

thank you very much

ADD REPLYlink written 5.1 years ago by A3.8k

http://genomespot.blogspot.com/2015/01/sra-toolkit-tips-and-workarounds.html

this link is useful too

ADD REPLYlink written 5.1 years ago by A3.8k

For converting to fastq directly

 fastq-dump --split-files --gzip
ADD REPLYlink written 3.6 years ago by Ron990
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1174 users visited in the last hour