Hey Martin

Thats exactly what I intended but sent it to general R list. Will post it
again. Thanks for checking.

-A

On Mon, Oct 24, 2011 at 2:32 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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/<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]]
>>
>> ______________________________**________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/**
>> posting-guide.html <http://www.R-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>

	[[alternative HTML version deleted]]

