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Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
I have come across several situations now where the `g_test` in the script `group_significance.py` gives implausibly small p-values. For instance, in a recent forum post, an individual was comparing two...
``` bash blab@blab:~/Desktop/Dehulajhari_HotSpring/qiime_analysis_F$ differential_abundance.py -i ucrss_iter/otu_table_mc2_w_tax.biom -o other_analysis/diff_otus.txt -m mapping.csv -a DESeq2_nbinom -c EC -x 0.019 -y 0.025 -d Traceback (most recent call last): File "/usr/local/bin/differential_abundance.py", line 5, in pkg_resources.run_script('qiime==1.9.1-dev',...
@gregcaporaso @wasade see below, I think this problem might also be affecting us http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html
The script `assign_taxonomy.py -m sortmerna` works great! However, the resulting taxonomy sometimes omits unassigned levels. In this output, `g__; s__` should be at the end of the second line, but...
Hi there I have a 288 multiplex 16S amplicon fastq file from MiSeq for which I have combined the reads and barcodes and removed unused barcodes. I have also validated...
The split_libraries.py script gives an option to count the consecutive number of bases falling below a quality score threshold. Users of UPARSE have an option to count total number of...
If the file specified via --sample_id_fp has blank lines, filter_samples_from_otu_table.py fails with an uninformative error message: ``` shell $ filter_samples_from_otu_table.py -i final_otu_table.biom -o site_C.biom --sample_id_fp Site_C.txt Traceback (most recent call...
I propose that `compare_alpha_diversity.py` should follow the format of `group_significance.py` in returning uncorrected AND corrected p-values. Currently, the return looks like (tab separated): `Group1 Group2 Group1 mean Group1 std Group2...
`qiime.filter.filter_mapping_file` is code that needs to be replaced. 1. **Documentation is actively misleading**: documentation says that the function removes metadata columns from the mapping file data if every sample to...