Question: Question: Convert .SRA to .FASTA
0
gravatar for Julian_R
22 days ago by
Julian_R0
Julian_R0 wrote:

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.

rna-seq • 126 views
ADD COMMENTlink modified 22 days ago by lieven.sterck8.7k • written 22 days ago by Julian_R0

I have also change the order of the command:

fastq-dump --fasta SRRNUMBER

but again, there is not .fasta file.

ADD REPLYlink modified 22 days ago • written 22 days ago by Julian_R0
1
gravatar for lieven.sterck
22 days ago by
lieven.sterck8.7k
VIB, Ghent, Belgium
lieven.sterck8.7k wrote:

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)

ADD COMMENTlink written 22 days ago by lieven.sterck8.7k

Many thanks!

I will try with that.

Regards.

ADD REPLYlink written 22 days ago by Julian_R0
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