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.

Thanks!
-Abhi

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