converting the format of read files in GEO datasets (SRA) to fasta and fatsq

Question

[zizigolu]

Hey guys,

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

Answer 1

[arnstrm]

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

[zizigolu]

Thank you very much

[zizigolu]

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

This link is useful too

[Ron]

For converting to fastq directly

 fastq-dump --split-files --gzip