Bumblebee

Data

• Location:

 /fs/szattic-asmg4/Bees/Bombus_impatiens

• There are 7 pairs of data files (paired ends) : lanes 1..3,5..8 (lane 4 wasn't used)

• 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.
 

• Data stats

 Lane   Insert   #Reads
 1      3Kbp     34,944,099 
 3      8Kbp     32,540,640

• Formatting: keep only the first 100bp

• circularization adaptors

 TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG - revcomp -> CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
 AGCATATTGAAGCATATTACATACGATATGCTTCAATAATGC

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