Banana Slug Genomics

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====== 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.

Banana Slug Genomics

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