Created
August 8, 2018 05:07
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mothur wrapper example
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| mothurDir <- '~/Downloads/mothur/' | |
| fastaFile <- './1060501B_cut3_without_N.fas' | |
| phylipFile <- paste(strsplit(fastaFile, '.fas')[1], '.phylip.dist', sep='') | |
| listFile <- paste(strsplit(fastaFile, '.fas')[1], '.phylip.fn.list', sep='') | |
| mothur(mothurDir, subfunc='dist.seqs', | |
| fasta=fastaFile, calc='onegap', cutoff=0.03, countends=F, output='lt') | |
| mothur(mothurDir, subfunc='cluster', | |
| phylip=phylipFile, | |
| method='furthest',cutoff=0.03) | |
| mothur(mothurDir, subfunc='bin.seqs', | |
| list=listFile, fasta=fastaFile) |
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