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
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
