Perl script error:syntax error near unexpected token `)'

Question

[slin023]

Greetings, I followed a Augustus manual to predict genome models. It seems reliable until I used perl command line to convert Isoseq alignment .psl to .gff using perl & blat2hints (P. 41). The command are the following:

 cat gmap.psl | sort -n -k 16,16 | sort -s -k 14,14 | perl -ne \
           ’@f=split; print if ($f[0]>=100)’ | blat2hints.pl --source=PB \
           --nomult --ep_cutoff=20 --in=/dev/stdin --out=isoseq.gff

but the I received the error shows -bash: syntax error near unexpected token('`.

Any ideas what is wrong with the command? please let me know, thank you!

Answer 1

[Mensur Dlakic]

I think that instead of ’ character it should be '.

'@f=split; print if ($f[0]>=100)'

[slin023]

ok, that works!! thank you so much! such a small detail makes difference!