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torognes / vsearch

Versatile open-source tool for microbiome analysis
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Include rows of OTUs with no mapped reads in OTU tables #517

Closed torognes closed 7 months ago

torognes commented 1 year ago

In cases were vsearch generates a OTU table, there might be some rows representing OTUs to which no reads map. As of now, these rows are not included in the OTU table. Perhaps all OTUs should be included, but with 0 for all columns (samples). This could be either default or optional.

torognes commented 7 months ago

Fixed in commit ca8cbd4.

When running the usearch_global or search_exact commands, samples and OTUs with no matches are now included in the OTU tables specified with the otutabout, biomout, and mothur_shared_out options. The corresponding columns and rows will all be zero.

torognes commented 7 months ago

Available in version 2.26.0, just released.