Question: Convert .SRA to .FASTA

Question

[DuanR]

Hello everyone,

I'm new in bioinformatics, so I would appreciate your help!

I have a small question, I would like to have a SRA file in two formats: FASTA and FASTQ. To download and to get the FASTQ has not been a problem, I use SRA toolkit (i.e. prefetch and fastq-dump). However, if I try to get (or convert) into FASTA format with SRA toolkit, nothing happens. I'm using:

fastq-dump myfile.sra --fasta

but there is not any FASTA document in my folder.

Thanks in advance!

Note: I'm using windows 10. I need FASTA because I'm doing BLAST with the BLAST+ package, and the input must be a .fasta.

[DuanR]

I have also change the order of the command:

fastq-dump --fasta SRRNUMBER

but again, there is not .fasta file.

Answer 1

[lieven.sterck]

You can use following program from BBMap suite.

reformat.sh in=your.fq out=your.fa

This will convert your fastq files into fasta format.

educational note: you could have find this easily by doing a search on google (and/or limiting to biostars.org)

[DuanR]

Many thanks!

I will try with that.

Regards.