**This is an old revision of the document!** ----
====== To Do ====== We went over some things that need updating in the wiki and plans for this weekend. * Document scripts added in [[computer_resources:bin|bin]] folder. * Find out which lanes in 454 run 3 are banana slug runs. But it turns out that this is not necessary: run "3" is not a separate run, but just run2 plus the non-banana-slug reads in other lanes. * Try mapping with Newbler or BWA. * BLAST/BLAT it. * Find insert lengths for the SeqPrep + Quake corrected Illumina data. * SOAPdenovo assembly try 1: * Only on Illumina data. * try 2: * Rank 1: All Illumina data as rank 1. * Rank 2: 454 data as rank 2 (both for contig building and scaffolding). * try 3: * Illumina + 454 data as rank 1. * # If insert length is negative, don't treat them as PE reads. * Newbler assemblies—no need for a new one, as there is no new 454 data. * Take another look at Barcode of Life mapping: [[http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG5|Invertebrate mitochondrial translation table]] * It turns out that blastall does not seem to have any documented way to tell tblastx to use a different genetic code, though the NCBI web server has the option. * The work Kevin did so far is now in assemblies/slug/barcode-of-life. * Next step is to use BWA to find all the SeqPrep+Quake treated Illumina reads that map to what has been found so far of the barcode. * Ed presenting paper on Wednesday. Get paper over the weekend.
