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lecture_notes:05-27-2011 [2011/05/27 20:29]
karplus fixed mistake on meaning of "rank 2". added info about barcode of life.
lecture_notes:05-27-2011 [2015/09/14 11:40] (current)
68.180.230.228 ↷ Links adapted because of a move operation
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-====== To Do ======+====== To Do (lecture notes) ​======
 We went over some things that need updating in the wiki and plans for this weekend. 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.+  * Document scripts added in [[archive:computer_resources:​bin|bin]] folder.
  
  
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   * try 3:   * try 3:
      * Illumina + 454 data as rank 1.      * Illumina + 454 data as rank 1.
-  * If insert length is negative, don't treat them as PE reads.+  * If insert length is negative, don't treat them as PE reads.   
 +    * This was an error in assumptions about what SOAPdenovo wants. ​ The number it wants is the total fragment length, which is what we are already estimating. ​ We just need to look at the average length for the pairs (based on the histogram) after SeqPrep. 
 +    * If Quake changes the distribution of reads (by trimming and discarding uncorrectable reads) it may be important to remap the new set of pairs to the 454 reads to get an improved estimate of fragment length.
   * Newbler assemblies—no need for a new one, as there is no new 454 data.   * 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]]   * Take another look at Barcode of Life mapping: [[http://​www.ncbi.nlm.nih.gov/​Taxonomy/​Utils/​wprintgc.cgi#​SG5|Invertebrate mitochondrial translation table]]
lecture_notes/05-27-2011.1306553399.txt.gz · Last modified: 2011/05/27 20:29 by karplus