Comparing two gff/gtf files : de novo transcripts v/s reference
On 10/24/2011 02:23 PM, Abhishek Pratap wrote:
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 [[alternative HTML version deleted]]
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