What sort of NGS did you use? How long are the reads? Sincerely, Adrian
On Sep 3, 2014, at 11:32 AM, "Boisvert, Sebastien" <boisv...@anl.gov> wrote: >> ________________________________________ >> From: Louis Letourneau [louis.letourn...@mail.mcgill.ca] >> Sent: Tuesday, August 26, 2014 8:52 AM >> To: denovoassembler-us...@lists.sf.net >> Subject: [Denovoassembler-users] Ray for HLA analysis >> 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?) > > > -graph-only > Exits after building graph. > > >> 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 > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ 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
