Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MicrobialDB does not include Human? #187

Open
rbtoscan opened this issue Oct 2, 2024 · 0 comments
Open

MicrobialDB does not include Human? #187

rbtoscan opened this issue Oct 2, 2024 · 0 comments

Comments

@rbtoscan
Copy link

rbtoscan commented Oct 2, 2024

Hi,

thank you for this very nice tool.
I want to use the MicrobialDB pre-built database to detect/quantify reads in my fastq files.
I am able to run the tool but it seems that the database and taxonomy file do not have the same tax IDs.

For instance, out of 58675642 reads, 54123119 (±92%) is classified as 9606, which I know it is human.
However, this tax id is not present in ktaxonomy.tsv file that is paired with the db.

I downloaded the DB and the indexes https://benlangmead.github.io/aws-indexes/k2:

https://genome-idx.s3.amazonaws.com/kraken/uniq/krakendb-2023-08-08-MICROBIAL/database.kdb
https://genome-idx.s3.amazonaws.com/kraken/uniq/krakendb-2023-08-08-MICROBIAL/kuniq_microbialdb_minus_kdb.20230808.tgz

I was hoping to find humans in both since it is in the description of the index:

image

Do you have maybe an up-do-date database by any chance? Or perhaps some directions to go about this?
Can I merge this ktaxnomy.tsv file with the nodes.dmp file from kraken2, remove duplicates and use it? Not sure if that would cause any issues.

Thank you.
Best
Rodolfo

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant