convert legacy blast parameters to blastn
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Entering edit mode
7.0 years ago
c.v.oflynn ▴ 100

Hi all,

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?

eg (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?

 

blast parameters • 1.8k views
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Entering edit mode
7.0 years ago
Siva ★ 1.8k

I think the -penalty option might be the culprit. When you change the -penalty value from default, you also need to set the supported values for -gapopen and -gapextend.

You can check the supported combinations here.

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Thanks Siva, helped a lot

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