andrewjmc

Preserve IDs

6

Hi Nick, Thanks for this tool. Is there any way to preserve the original GTDB taxids in the dmp files produced? There is no kraken2 GTDB 16S database. However there...

Standard taxonomy taking a long time for a single bin

5

## Expected Behavior I thought mmseqs would be quite quick to annotate a single MAG ## Current Behavior I am using the SemiBin GTDB database for mmseqs (https://zenodo.org/record/4751564/files/GTDB_v95.tar.gz) and standard...

Strange results

1

Hello, Thanks for this amazing tool. I am using fastv in perhaps an unusual way. I'm looking to detect the presence or absence of homologous gene clusters in metagenomic data....

Multinomial ebal NA weights - can't investigate

3

Hello again! ```test_weights_three_arm

Feature proposal: NAs

3

Hello, Thanks again for such a useful tool. It's my understanding from the code that any node with NAs for 50% or more descendants cannot be considered in the candidate...

kraken-filter

1

Hello, Is there any way to use kraken-filter from kraken 1 with kraken 2? This could allow quicker/less resource intensive experimentation with different confidence thresholds without having to rerun searches....

I have just noted that in my (heavily human dominated) pharyngeal swab sequence data, most of what I had annotated as contaminants (Decontam) are actually directly proportional to the abundance...

Multinomial treatments and CBPS

3

Hello, Is it possible to use/modfy treatSens to work with a multinomial treatment (three levels), which I have been analysing using CBPS? Thanks, Andrew

Threading

1

Hello, Really useful tool. Is this multi-threaded or single threaded? Thanks, Andrew

Hello, In comparing search results, I have noted significant disagreement between m/z as reported by MaxQuant and pFind (Spectra.mass/Charge). I have confirmed this in two separate studies. Of note, the...