Differences

This shows you the differences between two versions of the page.

--- lecture_notes:05-27-2011 [2011/05/28 03:25]
karplus mapping 454_run3 not needed.
+++ lecture_notes:05-27-2011 [2011/05/28 03:29]
karplus fixed mistake on meaning of "rank 2". added info about barcode of life.
@@ Line 12: / Line 12: @@
      * Only on Illumina data.
   * try 2:
-     * Rank 1: All Illumina data for contig building.
+     * Rank 1: All Illumina data as rank 1.
-     * Rank 2: 454 data for scaffolding.
+     * 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.
+  * 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