This solved my problem, thanks!
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Remote blast of SRA database
I am trying to use blast remotely using command line. I want to specify a certain database to blast, and I figured it out for WGS databases:
./blastn -db WGS_VDB://EXAMPLEID01 -query tmp.fa -out out.txt -remote
However, I don't know how to do it for SRA databases. Since it is possible to do it manually using the web interface, I figured that it should be possible to do it if I can specify the correct db name for the given SRA experiment.
Does anyone know how to do it and can provide an example?
Thanks!
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Brice Sarver
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emre.cto •
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The SRA-searching blastn is part of sra-tools.
Check out the blastn README on sra-tools' Github. Note that the SRA objects are prefetched.
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What exactly do you want to blast? SRA is a repository for NGS data from different published study consisting of petabytes of data.
I want to blast nucleotide coding sequence of a gene to a specific sequencing run. I don't want to blast to whole sra database, but rather specify an id like SRR1639025.