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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 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 for contig building.
    • Rank 2: 454 data for scaffolding.
  • try 3:
    • Illumina + 454 data as rank 1.
  • # If insert length is negative, don't treat them as PE reads.
  • Newbler assemblies.
  • Take another look at Barcode of Life mapping: Invertebrate mitochondrial translation table
  • Ed presenting paper on Wednesday. Get paper over the weekend.
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lecture_notes/05-27-2011.1306553117.txt.gz · Last modified: 2011/05/27 20:25 by karplus