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.
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written
by
DuanR •
1 answer
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)
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I have also change the order of the command:
fastq-dump --fasta SRRNUMBER
but again, there is not .fasta file.