Bumblebee: Difference between revisions
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2. GC bias, so we can compute a-stats properly | 2. GC bias, so we can compute a-stats properly | ||
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 | |||
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 = | = Assembly = | ||
Revision as of 03:29, 4 March 2010
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