Hi all,

I am confused with the "intron-redundant" meaning. My understanding is: the two transcript are differed only at one intron or exon with one end difference (-F). What is "-F" meaning here? Thanks!

cuffcompare

-C include the "contained" transcripts in the .combined.gtf file
-F do not discard intron-redundant transfrags if they share the 5' end
   (if they differ only at the 3' end))
-G generic GFF input file(s): do not assume Cufflinks GTF, do not
   discard any intron-redundant transfrags)