TaxID mapping file
0
0
Entering edit mode
6 weeks ago
Lada ▴ 30

Hi guys,

does anyone know how I get TaxID mapping file for NR or Uniprot database?

Background: I use Diamond for my de novo transcriptome annotation. My next goal is to use hits tsv file in blobtools for contamination detection. To do that I need my query transcript IDs with the corresponding subject TaxID in hits.tsv file. Diamond doesn't give that information but I can use blobtools taxify option to match corresponding TaxidIDs to my subject hits. I read blobtools documentation and to do that I need TaxID mapping file for the database that I used for annotation and that file consists of information such as.

in this example

I am not sure how to get that file so please help. :)

annotation blobtools RNAseq decontamination transcriptomes • 396 views
ADD COMMENT
1
Entering edit mode

nodesDB file should have been installed if you had used "Install" script for blobtools according to : https://blobtools.readme.io/docs/taxonomy-database

You can find the NCBI taxonomy database files here: https://ftp.ncbi.nih.gov/pub/taxonomy/ Take a look at https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt for the contents.

ADD REPLY
0
Entering edit mode

thank you, I'll look at these files/documents. .

ADD REPLY
0
Entering edit mode

if I understood correctly, I might need fle prot.accession2taxid.gz file? According to the documentation in column 2 is Accession.version and in column 3 is TaxID. I should download that file from NCBI, unpack it and than do:

blobtools taxify \ 
 -f diamond.out \
 -m prot.accession2taxid.taxids 
 -s 2 \ # column of sequenceID of subject in taxID mapping file
 -t 3 # column of TaxID of sequenceID in taxID mapping file

Does that make sense?

Did anyone try this?

I also saw this post about getting taxonomy info in Diamond output. Still, it seems it has to be incorporated in makedb step + I might be getting more than 1 taxid hit according to Diamond documentation which I am not sure might work with blobtools.

ADD REPLY

Login before adding your answer.

Traffic: 1931 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6