Comments (3)
Regarding COI, this is now covered under #56 --> the outputs are already in the required 7-levels.
Regarding 16S, we still wait for the Silva update. However, we have been waiting for a while and are getting a bit fed-up with waiting, hence it would be useful to do this ourselves. For advice on how to do this (and if it is feasible), consult with @hariszaf and @cpavloud
from pema.
Regarding the ITS gene and the Unite database: one thing you could do is to get the General FASTA release (download) file and from there get the sequences id.
For example:
>Glomeraceae|AM076560|SH146432.05FU|refs|k__Fungi;p__Glomeromycota;c__Glomeromycetes;o__Glomerales;f__Glomeraceae;g__;s__uncultured_Glomus
The AM076560
is the sequence id.
Using that, you can get from the NCBI the organism it comes from
https://www.ncbi.nlm.nih.gov/nuccore/AM076560
and therefore, its NCBI taxonomy id.
from pema.
may be some interplay with #29 here
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Related Issues (20)
- add remove_singletons option in OTU pipeline HOT 4
- Error when unzipping using a checkpoing HOT 1
- HPC job specifications HOT 4
- custom_ref_db doesn't work. HOT 5
- Upgrade to crest4
- extended final table HOT 1
- PEMA Ro-Crate HOT 1
- PEMA to create a run summary file HOT 2
- MIDORI updates HOT 2
- Unexpected Singletons in Final Table despite removeSingletons set to "Yes" HOT 5
- Error PEMA ASV inference: Directory swarm does not exists HOT 5
- 16s copy number
- When Swarm is chosen for the ITS, the names of the sequences are OtuXX and not ASVXX HOT 4
- Needed updates on "PEMA's output files.md" HOT 2
- time consuming preprocessing
- Storage usage of PEMA HOT 1
- pandaseq error "Something is wrong with this ID" HOT 17
- Long recurrent taxonomic labels HOT 1
- Wrong sample names in OutputPerSample HOT 5
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