Run Makeblastdb For Compressed File
Hi all, Does anyone know how to make database for compressed file fasta.gz using blast? I am using the blast2.2.29+. I saw the tutorial of makeblastdb, there is no option for dealing with the fasta.gz file. Does that mean I have to unzip the file first and then build database?
1 answer
You should be able to uncompress the file then pipe the output to makeblastdb, without an intermediate file. The command would look something like:
gunzip -c myfastafile.gz | makeblastdb -in stdin <other options>
or
gunzip -c myfastafile.gz | makeblastdb -in - <other options>
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