Comparing two gff/gtf files : de novo transcripts v/s reference

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Hi All

I am wondering if people based on their experience could share what methods
one could use to compare two gff/gtf files. The reason why I want to do so
is that we have constructed a RNA-Seq based transcriptome  and would like to
compare it with reference transcriptome we had from in-silico approaches.
Ideally we are looking to find out

1. new genes  we see
2. transcripts where the start/end side is changed (upstream/downstream)
3. possible gene fusions may be because in-silico approaches were not
correct

I know some of these could be resolved with BedTools but just wondering if
Bioconductor has anything specific built in coz each time it pleasantly
surprises me.
Hi Abhi --

better to ask on the Bioconductor mailing list

http://bioconductor.org/help/mailing-list/

where people will point to rtracklayer to import() gff files, and 
GenomicRanges to do the types of comparisons you're interested in. These 
will generally be fun and performant tools.

Martin
Thanks!
-Abhi

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