Version Differences for PacBioToCA

(→Summary)
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  In running pacBioToCA, we found that the amount of PBcR was influenced by the parameter of genomeSize, especially when the coverage of PacBio RS data was high (>50X).    In running pacBioToCA, we found that the amount of PBcR was influenced by the parameter of genomeSize, especially when the coverage of PacBio RS data was high (>50X). 
       
- Short reads: 118X, long reads: one ~ four SMRT cell reads, w/wo genome size   + Short reads: 118X, long reads: one ~ four SMRT cell reads, with/without genome size.  
       
       
       
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    + Here, we adjust Celera Assembler parameters to make overlap detection more stringent ([http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA ref]).  
  runCA unitigger=bogart merSize=14 ovlMinLen= <ovl value> utgErrorRate=0.015 utgGraphErrorRate=0.015 utgGraphErrorLimit=0 utgMergeErrorRate=0.03 utgMergeErrorLimit=0 -p asm -d asm viaMiseq.frg    runCA unitigger=bogart merSize=14 ovlMinLen= <ovl value> utgErrorRate=0.015 utgGraphErrorRate=0.015 utgGraphErrorLimit=0 utgMergeErrorRate=0.03 utgMergeErrorLimit=0 -p asm -d asm viaMiseq.frg 
       
- The <ovl value> parameter was set to approximately 40% of your average corrected sequence lengths ([http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA ref]). ''As a general rule, if the average corrected length is less than 2.5Kbp, set it to 1000, if it is less than 3Kbp, set it to 1500, if it is less than 5.5Kbp, set it to 2000, if it is greater than 5.5Kbp, set it to 2500, and if it is greater than 6.5Kbp, set it to 3000.''   + The <ovl value> parameter was set to approximately 40% of your average corrected sequence lengths. ''As a general rule, if the average corrected length is less than 2.5Kbp, set it to 1000, if it is less than 3Kbp, set it to 1500, if it is less than 5.5Kbp, set it to 2000, if it is greater than 5.5Kbp, set it to 2500, and if it is greater than 6.5Kbp, set it to 3000.''  
       
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