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.

• Lane 1: 3Kbp insert; 34,944,099 reads
• Lane 3: 8Kbp insert; 32,540,640 reads

• Formatting:

 /fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/fastqToCA \
   -insertsize 3000 300 \
   -libraryname 1 \
   -type illumina \
   -fastq /fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_1_sequence.txt,/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_2_sequence.txt > 1.frg
 =>
 {LIB                                                                                                                                      
 act:A                                                                                                                                     
 acc:1                                                                                                                                     
 ori:I                                                                                                                                     
 mea:3000.000                                                                                                                              
 std:300.000                                                                                                                               
 src:                                                                                                                                      
 .                                                                                                                                         
 nft:10                                                                                                                                    
 fea:                                                                                                                                      
 forceBOGunitigger=1                                                                                                                       
 isNotRandom=0                                                                                                                             
 doNotTrustHomopolymerRuns=0                                                                                                               
 doRemoveDuplicateReads=0                                                                                                                  
 doNotQVTrim=0                                                                                                                             
 goodBadQVThreshold=0                                                                                                                      
 doNotOverlapTrim=0                                                                                                                        
 usePackedFragments=1                                                                                                                      
 illuminaFastQType=illumina                                                                                                                
 illuminaSequence=/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_1_sequence.txt,/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_2_sequence.txt    
 .                                                                                                                                         
 }

 rm -fr asm.*
 /fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/gatekeeper \
   -o /scratch1/Bombus_impatiens/Assembly/1.redo/./asm.gkpStore.BUILDING \
   -T  -F  \
   -E /scratch1/Bombus_impatiens/Assembly/1.redo/./asm.gkpStore.errorLog \
   /scratch1/Bombus_impatiens/Assembly/1.redo/1.frg 
 => Segmentation fault

Assembly

 /fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/runCA