Generally you'll want to use the same version that everyone else you're working with is using. If that's not an issue go with hg19, it's better at the sequence level, and the annotations on it are getting deep enough you can interpret most things against them.
On Dec 18, 2009, at 8:01 PM, S. Sun wrote: > Hello, > > I am a beginner of sequencing data analysis. I want to do alignment > for > Illumina chip-seq data using bowtie. Does anyone know which human > genome > reference shall I align against? Hg19 or Hg18? > > Thanks for your attention. > > Sun > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
