[BioC] exon exon junction library for human

[Steve Lianoglou]

Hey,

Sorry, that splices file was actually made against the unmasked hg19  
fasta file.

I'm not sure, but you might have to make your own hg19 database for  
cistematic at some point down the road, so you might want to do that  
know and build your own splices file anyway. But that's certainly your  
choice ...

-steve

On Aug 20, 2009, at 11:58 AM, shirley zhang wrote:

> Thanks. I am planing to use ERANGE and TopHat.  Your file will  
> definitely help, especially it is against the human hg19/NCBI37  
> genome.
>
> Thanks again,
> Shirley
>
> On Thu, Aug 20, 2009 at 11:52 AM, Steve Lianoglou <mailinglist.honeypot at gmail.com 
> > wrote:
> Hi,
>
>
> On Aug 20, 2009, at 11:46 AM, shirley zhang wrote:
>
> Hi Steve,
>
> Thank you for your quick response.
>
> If you can share your file with me, that would be fantastics.
>
> You can get the file here:
>
> http://cbio.mskcc.org/~lianos/files/hg19_splices.fa.zip
>
> That was created with the hg19/masked fasta files. The leading and  
> trailing NN-dinucleotides from each sequence were inserted by ERANGE.
>
> I'm actually not sure that this file will help you directly unless  
> you're planning to use ERANGE's pipeline, though.
>
> -steve
>
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  |  Memorial Sloan-Kettering Cancer Center
>  |  Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
>
>
>
> -- 
> Xiaoling (Shirley) Zhang
>
> Ph.D. Candidate in Bioinformatics
> Boston University, Boston, MA
> Tel: (857) 233-9862	
> Email: zhangxl at bu.edu

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact