Message-ID: <4EA5D954.2090905@fhcrc.org>
Date: 2011-10-24T21:32:04Z
From: Martin Morgan
Subject: Comparing two gff/gtf files : de novo transcripts v/s reference
In-Reply-To: <CAJbA1KC6X7h9aiuKdXPA-+-hxKwT7BUVy+qZ9yVMJ0ryHFttMQ@mail.gmail.com>
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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