how to use Lastz "multiple contains"?

Question

[panly89]

Hi, everyone. I want to do two genome sequence alingment by Lastz software, but in my fasta files, the sequence data was separated by chromosome, not one sequence, how to use the "multiple" contian? I used the sentence

lastz a.fasta[multiple ]* b.fasta[multiple]* --notrasition --step=20 --nogapped --format=maf >a_b.maf

but tell me error the a.fasta not the end", WHY? please give me a hand, thank you very much ~~

[panly89]

it will be the best, give me the right comment line~thank you

[madzayasodara]

Hey! Did you figure this out? I have the same issue.

Answer 1

[AK]

Hey panly89, try removing the asterisks:

lastz a.fasta[multiple] b.fasta[multiple] --notrasition --step=20 --nogapped --format=maf > a_b.maf