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==Objectives== *Test on proportional sampling size #Sampling 1000 reads for the lowest number group. #Sampling the proportional number of reads for other groups based on fold variance. *Test different blastn parameter settings: #Expectation value 10(default) => -e 0.01 #blastn DUST filter T(default) => F ===Test of -e parameters=== *No bad alignment structure was found using default -e 10 setting. *No difference on output results was observed by switching between -e 0.01 and -e 10. **It is probably due to that I used the blastn setting that only report the best hits. **I will switch to use -e 0.01 anyway for future blastn. ===Test of -F parameters=== *Turning off DUST-filter(FF) increase 10% hit compared to filter-on setting(FT) *However some data have problems to be run with FF setting. Error message: "Program failed, try executing the command manually.". *The problem sometime could be solved by changing the file name. *I need to do more tests to figure out why, but current I decide to keep using FT(default) for all of my blastn analysis.
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