Hello, I currently try to create a shell script to run a blast and then to align the result of my blast Here is the beginning of my script :
$1 -query $2 -db $3 -outfmt 6 -remote | awk '$3>95' > $4
Im not sure about the begining. Furthermore, i really dont know how i can, from my blast result extract the sequences and put them in a fasta file to run the alignement. Samtools ? I'd like to run the alignement using MAFFT.
can you help me ? Thanks a lot , iam really bloqued for now...