[BioC] exon exon junction library for human

[Steve Lianoglou]

Hi Shirley,

On Aug 20, 2009, at 11:21 AM, shirley zhang wrote:

> Dear List,
> I am working on a next generation sequencing data set from Human. I am
> wondering whether there is a public exon-exon junction library  
> available.

I'm not sure if I get what you mean, but perhaps this might help.

I recently got ERANGE[1] working for some RNA-seq analysis. Part of  
the preliminary steps is to creata a fasta file that has sequences  
spanning known exon/exon junctions.

If you want to make such a file, read the instructions in the  
README.build-rds.txt file of the ERANGE package.

That having been said, I've built such a file for 32bp reads against  
the human hg19/NCBI37 genome which I can give you, if you like (with  
the disclaimer of not being held responsible if that file is actually  
wrong).

-steve

ERANGE: http://woldlab.caltech.edu/rnaseq/

--
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