Bumblebee: Difference between revisions

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= Data =
= Data =


* Location:
* ~ 500B genome
  /fs/szattic-asmg4/Bees/Bombus_impatiens
 
* 7 pairs of data files (paired ends) : lanes 1..3,5..8 (lane 4 wasn't used)


* There are 7 pairs of data files (paired ends) : lanes 1..3,5..8 (lane 4 wasn't used)
  Lane  Insert            ReadLen    #Reads
  1      3Kbp(2..6,avg 4) 124        34,944,099
  2      8Kbp(7..9,avg 8)  124        32,540,640
  3     gDNA              ~500      34,745,750
  5     gDNA                        34,601,239
  6      gDNA                        34,553,857
  7      gDNA                        34,682,612
  8     gDNA                        12,975,839


* Tasks to figure out:
* Tasks to figure out:
Line 11: Line 20:
  3. Redundancy in the long paired ends, which are lane 1 and lane 2.
  3. Redundancy in the long paired ends, which are lane 1 and lane 2.
    
    
* Data stats
* Used the 454 protocol to circularize the DNA for sequencing with the Illumina instrument. 
  Lane  Insert  #Reads
** Some reads will begin in the circularization adaptor and thus will have only one usable read
  1      3Kbp    34,944,099
** Some reads have a few bases of DNA sequence and hit the circularization adaptor right away
  3      8Kbp    32,540,640
** Most reads will have at least 36bp from each end before hitting the adaptor.
 
** Many reads will not have any adaptor to trim (>125bp of DNA sequence at both ends of the adaptor)
* Formatting: keep only the first 100bp


* circularization adaptors
* circularization adaptors
   TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG - revcomp -> CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
   TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG - revcomp -> CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
   AGCATATTGAAGCATATTACATACGATATGCTTCAATAATGC
   AGCATATTGAAGCATATTACATACGATATGCTTCAATAATGC
* Formatting: keep only the first 100bp (last 24 bp are anyway low qual)
* Location:
  /fs/szattic-asmg4/Bees/Bombus_impatiens


= Assembly =
= Assembly =

Revision as of 15:20, 4 March 2010

Data

  • ~ 500B genome
  • 7 pairs of data files (paired ends) : lanes 1..3,5..8 (lane 4 wasn't used)
 Lane   Insert            ReadLen    #Reads 
 1      3Kbp(2..6,avg 4)  124        34,944,099 
 2      8Kbp(7..9,avg 8)  124        32,540,640

 3      gDNA              ~500       34,745,750 
 5      gDNA                         34,601,239
 6      gDNA                         34,553,857
 7      gDNA                         34,682,612
 8      gDNA                         12,975,839
  • Tasks to figure out:
1. Erroneous reads/bases, which we need to correct or discard
2. GC bias, so we can compute a-stats properly
3. Redundancy in the long paired ends, which are lane 1 and lane 2.
 
  • Used the 454 protocol to circularize the DNA for sequencing with the Illumina instrument.
    • Some reads will begin in the circularization adaptor and thus will have only one usable read
    • Some reads have a few bases of DNA sequence and hit the circularization adaptor right away
    • Most reads will have at least 36bp from each end before hitting the adaptor.
    • Many reads will not have any adaptor to trim (>125bp of DNA sequence at both ends of the adaptor)
  • circularization adaptors
 TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG - revcomp -> CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
 AGCATATTGAAGCATATTACATACGATATGCTTCAATAATGC
  • Formatting: keep only the first 100bp (last 24 bp are anyway low qual)
  • Location:
 /fs/szattic-asmg4/Bees/Bombus_impatiens

Assembly

  • Meryl
 meryl -Dh -s 0-mercounts/asm-C-ms22-cm1 >! 22mers.hist
 Found 3136399464 mers.
 Found 379123530 distinct mers.
 Found 201257394 unique mers.
 Largest mercount is 12006651; 90 mers are too big for histogram.
  • countKmers
 most frequent 22mer :                 AGCATACATTATACGAAGTTAT     ~ 16% of the seqs
 most frequent 42mer : CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA ~ 10%  of the seqs (pPAC7.9124-9165)  
 
  • Location
 /fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/runCA