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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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head mergers issue. #377

Closed IrshadUlHaq1 closed 6 years ago

IrshadUlHaq1 commented 6 years ago

Is it unusual to see this variation in the abundance column?

head(mergers[[1]]) sequence 1 TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGTGGTTCTTTAAGTCTGATGTAAAAGGCAGTGGCTCAACCATTGTAGGCATTGGAAACTGGGGAACTTGAGTGCAGTAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGAGGCGAAAGCGGCTCTCTGGGCTGTAACTGACACTGAGGCTCGAAAGCGTGGGTAGCAAACAGG 2 TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCGAAACTGGCAGGCTTGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG 3 TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCGAAACTGGCAGGCTTGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCAAAAGCGTGGGGAGCAAACAGG 4 TACGGAGGGTGCAAGCGCTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCGAAACTGGCAGGCTTGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACCGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG 6 TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGCCTGATAAGTCAGATGTGAAATCCCCGAGCTCAACTTGGGAACTGCGTTTGAAACTATCAAGCTAGAATATGTCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCAATGGCGAAGGCAGCCCCCTGGGATAATATTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGG 7 TACGTAGGGTGCGAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTTTGTCGCGTCTGTCGTGAAAGTCCGGGGCTTAACCCCGGATCTGCGGTGGGTACGGGCAGACTAGAGTGCAGTAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAGGAACACCGATGGCGAAGGCAGGTCTCTGGGCTGTAACTGACGCTGAGGAGCGAAAGCATGGGGAGCGAACAGG abundance forward reverse nmatch nmismatch nindel prefer accept 1 11299 1 1 148 0 0 2 TRUE 2 2804 2 2 147 0 0 2 TRUE 3 88 18 15 147 0 0 2 TRUE 4 85 11 16 147 0 0 2 TRUE 6 44 3 3 147 0 0 1 TRUE 7 28 4 4 147 0 0 2 TRUE

benjjneb commented 6 years ago

From that it looks like you have a quite dominant top taxa (or two) in this community. But, microbial communities come in all "shapes and sizes" so I don't know if that would be usual or unusual for the environment you are studying.