Hi All-
I have some V9 amplicon Miseq and Hiseq metagenomic data that I have been processing in Qiime that I am trying to filter my OTU table to only contain OTU's that are at least 0.01% abundant in a given sample in a data set.
Searching online I found filter_otus_from_otu_table.py but this removes any OTU that is less than the given threshold within the whole data set. Therefore, the whole OTU is removed from the table. My issue is that an OTU might be below 0.01% in the given whole data set but might be a higher percentage within a certain sample within the data set. Therefore, I am losing wanted/ keeping unwanted information within my OTU table by completely removing an OTU based on the abundance in the data set. Also results might change based on what samples I include in the whole data set.
I have also found filter_otus_by_sample.py but this is in order to remove certain samples from the OTU table. I do not want to remove a certain sample just want to remove counts of OTUs from a sample that is below a given threshold.
Does anyone know of a script that will look through a OTU table sample by sample and remove OTU counts for abundances below a certain threshold? (change counts to 0 if below the threshold and remove OTU's that are zero across all samples).
Thanks in advance
I have some V9 amplicon Miseq and Hiseq metagenomic data that I have been processing in Qiime that I am trying to filter my OTU table to only contain OTU's that are at least 0.01% abundant in a given sample in a data set.
Searching online I found filter_otus_from_otu_table.py but this removes any OTU that is less than the given threshold within the whole data set. Therefore, the whole OTU is removed from the table. My issue is that an OTU might be below 0.01% in the given whole data set but might be a higher percentage within a certain sample within the data set. Therefore, I am losing wanted/ keeping unwanted information within my OTU table by completely removing an OTU based on the abundance in the data set. Also results might change based on what samples I include in the whole data set.
I have also found filter_otus_by_sample.py but this is in order to remove certain samples from the OTU table. I do not want to remove a certain sample just want to remove counts of OTUs from a sample that is below a given threshold.
Does anyone know of a script that will look through a OTU table sample by sample and remove OTU counts for abundances below a certain threshold? (change counts to 0 if below the threshold and remove OTU's that are zero across all samples).
Thanks in advance
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