I am following the parameters given in a paper for performing blast.
The parameters given are in the old format;
-X 150 -q -1 -F F
Could anyone convert them to the current blastn format?
e.g., (throws errors);
-xdrop_gap_final 150 -penalty -1 -dust no
I could use the old blast, but I am also using
-outfmt "6 std qlen qcovs"
which I don't think is possible for old format?