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### Is your feature related to a problem?
I often want to find the sequence that was used for a particular assignment. I especially want to be able to do this when using the workflow with students to…
irc47 updated
3 weeks ago
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Hi @benjjneb this isn't an issue with dada2 but more a general question. We're using a slightly modified version of the big data workflow implemented in Nextflow for processing PacBio data, but the k…
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I am analyzing ITS1 amplicon data using DADA2 and the UNITE reference database. Last week I had an issue where the assignTaxonomy function was labeling ASVs as outlandish taxa (telling me I had marine…
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Hello! I was using this package to generate OTU assignments and to understand the communities for a set of metagenomic raw reads that I have. While converting the table to a wide format suitable for p…
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Hello,
I am running lotus2 only for taxonomy assignment of ITS1 sequences (so -taxOnly) (which is great! works super fast). I assumed that the output file would contain the same number of sequences…
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Dear Chris,
I've been trying to run DESMAN on some of my own data but I keep getting errors during the contig taxonomy assignment step described in your complete example. Specifically the ClassifyC…
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When I try to run matam_assembly.py from the conda installation MATAM, I get an error that it doesn't recognize an option `--perform_taxonomic_assignment`. Does conda version not include this option?
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Hello,
I am trying to work through the pipeline, but it appears to be getting stuck somewhere during VSEARCH. I ran the following code and got this message:
snakemake --jobs 20 --snakefile snake…
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Hi @jenniferlu717,
Since Bracken calculates the probabilities of taxonomic assignment at different levels for reads of a certain length using the default Kraken2 confidence threshold of 0 during the …
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I downloaded all non-_K. pneumoniae Klebsiella_ data from v0.1.
I used the equivalent of the v0.2 species_calls.tsv.gz file to identify all _Klebsiella._ I then stripped out the species I didn't wa…