Reference GTF file - combine several files?

[Sabine_Holz]

Dear all,

I need a reference GTF file for Cufflinks package, but I have 5 single GTF files.

Is it possible to merge these files to 1 GTF file? How?

Does this GTF file automatically fit to the referring index which was used for TopHat calculation?

Thanks a lot in advance!

[dpryan]

Were the 5 GTF files previously generated by cufflinks (in which case, just use cuffmerge)? Otherwise, the question becomes why you would want to merge them.

[GenoMax]

http://seqanswers.com/forums/showthread.php?t=15115

[Sabine_Holz]

I need a GTF file for my reference (cucumber); but mitochondrion and mitochondrion are excluded from that GTF file. So I need to merge them

5 individual GTF = 1 combined GTF for reference

[TiborNagy]

BedTools is what you need.