Flair error in nanopore data

Question

[bioinfo_ga]

Hi all

I am performing alternative splicing for nanopore data using tool FLAIR. In that there is a module, "find_alt3prime_5prime_ss.py" where i am getting continous error regarding usage. usage: script.py isoforms.psl colnum alt_acceptor.txt alt_donor.txt Can anyone elaborate the colnum parameter in command i tried giving last 2 column numbers of read count from isoform.psl file but error still persists.

Thanks...

[Buffo]

The FLAIR page said that the running mode is:

python find_alt3prime_5prime_ss.py isoforms.psl colnum1 colnum2 alt_acceptor.txt alt_donor.txt

Are you running it in that way?