-
I am trying to count the assignments at each level and use tax_glom to summarise the tax_table. But tax_glom() with rank_names[1] throws an error.
``` S
myData
```
```
phyloseq-class experiment-leve…
-
https://github.com/RNAcentral/rnacentral-import-pipeline/pull/12 got merged recently.
-
Hi
When i ran "The de novo workflow" process, it showed error messages as below:
[2018-03-16 23:30:12] INFO: GTDB-Tk v0.0.4b3
[2018-03-16 23:30:12] INFO: gtdbtk de_novo_wf --genome_dir my_genome …
-
This is a common request, and an area where the high-resolution offered by dada2 really should be leveraged.
The current plan is for a new function `assignSpecies` which takes a taxonomic table creat…
-
Hi there,
Sorry for posting a very basic question.
I am using mothur to process my 16SV4 data. From my output file -"16S.final.an.unique_list.0.03.cons.taxonomy (TAXONOMY file)", I found that whi…
-
Hello,
I am trying to run taxon profile but I am finding problems to do it:
I will add detailes here:
STDOUT file:
starting taxon_profile
Thu May 17 02:58:00 CEST 2018
[2018-05-17 02:58:01] …
-
Hey,
I classified my 16S reads with "kraken2 --db $DB_Silva --threads 5 --output $out/20170519_Silva.kraken --report $out/20170519_Silva.mpareport --use-mpa-style $infile1". Although I got a normal…
-
-
Using DADA2 is it necessary to extract the ITS region using something like ITSx( http://microbiology.se/software/itsx/) prior to taxonomic assignment? If so how would one go about this?
-
Hi, great package. I am using it to fix/define taxonomic assignments from a Silva 18s database. The dmp files that I just downloaded seem to have slightly different accession numbers than the Silva d…