User Tools

Site Tools


lecture_notes:05-27-2011

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 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: 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.
You could leave a comment if you were logged in.
lecture_notes/05-27-2011.1306553399.txt.gz · Last modified: 2011/05/27 20:29 by karplus