I was wondering if someone would have ideas/insight on how to apply Ray (colored debruijn graph) to HLA analysis.
Bit of background (skip this if you want to skip to the Ray part): ---> HLA are genes is a region of the human genome (MHC region) that is highly polymorphic. There are 2 classes of genes in the MHC region. Genes that are interesting are usually HLA-A, HLA-B, HLA-D* These are important for individual typing for organ donations, skin graph, etc, etc. There are over 12,000 differently known/reported alleles (between genes) in this region. There are typically 2 techniques to target this region, either target some key regions (incomplete but good enough), or sequence the whole thing. ---> There many tools that kind of do this, but they all have problems. I am trying Ray communities and Ray surveyor for this but I'm wondering which would be better suited (before I get my results) for this task Communities using the known alleles as a reference set or Surveyor using kmers built for each alleles as reference set. (also is there a way to get ray to just build the kmers.txt file without doing the rest?) What are your thoughts, if thoughts you have :-) Thanks Louis ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
