Comments (2)
Also would be helpful to have log information for how many ASVs and what abundance of reads were excluded.
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Added feature to exclude ASVs with NSTI > 2 by default in metagenome_pipeline.py
in this PR: #17.
Outputting log information would still be useful.
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Related Issues (20)
- File "pandas/_libs/parsers.pyx", line 1973, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: EOF inside string starting at row 37 HOT 3
- what is the mean of the column name“taxon_rel_abun/genome_function_count/taxon_function_abun/taxon_rel_function_abun” in the KEGG_pathways_out/path_abun_contrib.tsv.gz/path_abun_contrib.tsv HOT 1
- MemoryError HOT 4
- add_descriptions.py does not work for stratified file HOT 2
- Question about Taxonomic info HOT 2
- Command error about picrust2 ? HOT 2
- Question about the methods of Hidden-state prediction HOT 1
- Requirement for fasta sequences and questions for when using Nanopore 16S data HOT 1
- object 'p_values_df' not found (error) HOT 2
- issue downloading Picrust
- pytest fails tests/test_place_seqs.py HOT 1
- How to use a custom KEGG database? HOT 1
- biom-format not found HOT 2
- Error of running picrust2_pipeline HOT 3
- how long should full pipeline command run? HOT 1
- de-novo clustered ASVs as input sequences in picrust2 HOT 1
- 3,751 input sequences aligned poorly to reference sequences and removed. HOT 1
- Analyzing Oxford Nanopore 16s data with Picrust2 HOT 1
- Error with hsp.py step with tutorial data HOT 3
- Does PiCrust2 generate 16S taxonomic classifications using your reference tree? HOT 3
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