[mattanswers]

I would also be very interested in generating a gtf file for arabidopsis. Would it be possible to post the code ?

[celeste8]

Download TAIR10_GFF3_genes.gff inTAIR, and then use the Perl script below to convert this gff file to gtf which is used as conference annotation Cufflinks.

#!/usr/bin/perl

use warnings;
use strict;
while (<>) {
chomp;
my @parts = split /\t/;
if ( !(($parts[2] eq 'three_prime_UTR')|($parts[2] eq 'five_prime_UTR')|($parts[2] eq 'exon')|($parts[2] eq 'CDS')) ) {
next;
}
elsif ( $parts[2] eq 'three_prime_UTR') {
$parts[2] = '3UTR';
}
elsif ($parts[2] eq 'five_prime_UTR') {
$parts[2] = '5UTR';
}
$parts[8] =~ s/^Parent=((\w+)\.\w*).*/gene_id \"$2\"; transcript_id \"$1\";/sg;
$_ = join "\t" , @parts;
print "$_\n";
}

[mattanswers]

celeste8, thank you very much !

[samhokin]

Thanks, celeste8!!