Open fconstancias opened 1 year ago
Sorry for the delay.
For the length information you can get them from here: https://ezmeta.unige.ch/CMMG/Supplementary_Tables_and_Figures/Tables/Table_S3_genome_info.tsv
I just uploaded my begin of making a package with all the utility function for this analysis to CMMG_tools There you have the function load_taxonomy
In order to aggregate the Kraken table you need first make the back mapping from species to representative genome. The following function should do this:
import pandas as pd
def rename_kraken_table(kraken_table,Tax): """ Kraken table that is at species level map to species indexes """
assert kraken_table.columns.is_unique
# create mapping of species to index
species2ref= pd.Series(Tax.index,Tax.species)
# remove redundant species
species2ref = species2ref.loc[~species2ref.index.duplicated(keep='first')]
kraken_table.columns = species2ref.loc[kraken_table.columns]
(Let me test this function once again)
- What exactly do you mean by the confidence threshold? This is a parameter for?
I apologize, I would make the code much smoother but for now I don't have so much time.
Dear @SilasK,
Thanks for the details.
What exactly do you mean by the confidence threshold? This is a parameter for?
Please see --confidence
from the manual or here. It might not be that important for habitat specific database but I was wondering whether you experiemented a bit using cmmg.
Best.
No I haven't used the confidence score. do you usualy use it?
I have been previously working with environmental samples using kraken refseq database and used --confidence
of 0.1 based on some results here. Using cmmg on mice GIT metagenomes it might not be needed, I have run the kraken2+bracken pipeline using --confidence
values of 0, 0.05, 0.1 and 0.2, and can share the results when I am there.
Hi @SilasK and @fconstancias,
I'd love to have your input on this https://github.com/DerrickWood/kraken2/issues/265#issuecomment-1285615638
cheers
HI @jorondo1,
Sorry for the delay, check AGalanis97 answer there.
Dear @SilasK,
Thanks for hard work on the field!
I am analysing mouse metagenome dataset and trying different tools & appraoches for an exhaustive characterisation of the taxonomic composition of the fecal metagenomes (i.e., metaphlan4, mOTUS, kraken-braken on CMMG)
I have 3 questions (so far) regarding the kraken pipeline:
--confidence
when working with CMMG and mice fecal metagenomes?Thanks for your help.
Best,
Florentin