Make a new directory for diamond:
cd mkdir diamond cd diamond
Download diamond:
wget http://github.com/bbuchfink/diamond/releases/download/v0.7.9/diamond-linux64.tar.gz tar xzf diamond-linux64.tar.gz
Put diamond in your path:
export PATH=$PATH:$HOME/diamond echo 'export PATH=$PATH:$HOME/diamond' >> ~/.bashrc
Download the swissprot database:
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz gunzip uniprot_sprot.fasta.gz
Index the database:
diamond makedb --in uniprot_sprot.fasta -d uniprot_sprot
Link in the fasta:
ln -s /salmon/nema_inList.fa mkdir ./tempDir
Run Diamond:
diamond blastx -d uniprot_sprot -q /mnt/data/nema_inList.fa -a matches -t tempDir -p 16
Convert to blast tab-separated output format:
diamond view -a matches.daa -o matches.m8