I'm trying to blast a dataset of gRNA against all the sequences present on the NCBI coming from Anopheles gambiae species. This is the script that I used:
blastn -db nt -query candidategRNA.fasta -task blastn-short -remote -evalue 10 -entrez_query 'Anopheles gambiae [organism]' -outfmt 6 -out G3-ill-G3-Nano-results.table
Blast is creating the output file but it's empty... I already tried to blast my gRNAs manually and I always found matches with the web-browser Blastn version....
There is a way to use blast against all the sequences belonging to a specific organism and not just against the reference genome assembly (in my case Agamp3) ?
Or do you know how I can create my local database importing all the sequences belonging to Anopheles in the NCBI archive?
Thanks in advance!