How to

Revision as of 24 July 2013 21:08 by admin (Comments | Contribs)

1 基本用法 runCA with asm.spec

   runCA -p asm -d asm -s asm.spec PBcR.viaMiseq.frg > asm.out 2>&1

2 web 提供，RunCA with parameters，有指定merSize=14:

   runCA unitigger=bogart merSize=14 ovlMinLen=2000 utgErrorRate=0.015 utgGraphErrorRate=0.015 
   utgGraphErrorLimit=0 utgMergeErrorRate=0.03 utgMergeErrorLimit=0 -p asm -d asm asm.overCov.frg

3 Paper Script提供(asmCorrected.sh), RunCA with asm.spec and parameters： 照asmCorrected.sh上面的順序不會work，後來依照runCA 指令說明去放=> usage: runCA -d <dir> -p <prefix> [options] <frg> 就ok了。 並且使用wgs-package提供的asm.spec提供 D:\Boss Jade\201306\20130614_Hybrid assembly to_do_list\Filter_good_long_read\wgs-package\doc 但記得將grid 設0和 sge 關掉(mark掉)

   runCA -p asm -d asm -s asm.spec unitigger=bogart utgErrorRate=0.015 ovlMinLen=2000 ovlErrorRate=0.03 cgwErrorRate=0.10 cnsErrorRate=0.10 
   utgGraphErrorLimit=0 utgGraphErrorRate=0.015 utgMergeErrorLimit=0 utgMergeErrorRate=0.03 asm.overCov.frg