phylogenetic tree

[BouchraChaouni]

Request:
Dear EBI Metagenomics Team,
I have a request about the phylogenetic tree related to my work.
When I downloaded the file where it's mentioned phylogenetic tree under Taxonomic Analysis for instance in this page for OSD24: https://www.ebi.ac.uk/metagenomics/projects/ERP009703/samples/ERS667644/runs/ERR771021/results/versions/2.0#ui-id-6 I got numbers as leaf IDs when I visualise the tree, instead of the taxonomic name.
What can I do to get the correct phylogenetic tree visualization?
PS: I used Fig Tree and iTOL

Solution: [email protected]
Dear Bouchra,
thanks for contacting us. The numbers used as leaf IDs are the OTU numbers and you can get the corresponding taxonomy assignments from the 'OTUs, reads and taxonomic assignments.tv' file. We display it this way as not all taxonomy assignments are at the same taxonomic level. However
if you would like to replace the OTU number in the tree by the corresponding OTU assignments, you can do so by following these steps:

• open the ERR771021_MERGED_FASTQ_pruned.tree file using a text editor (on Windows, avoid Word) then for clarity replace the commas by line returns. You will then have a file with 359 lines
• open the ERR771021_MERGED_FASTQ_otu.tsv file. The first column is the OTU number, the second the count and the third is the corresponding taxonomy assignments. For display purpose, extract the more precise taxonomic terms for each OTU
• replace the OTU numbers in ERR771021_MERGED_FASTQ_pruned.tree file with the extracted taxonomic terms surrounded by single quote.
• replace all line returns back by commas. Save the file.
• re-open in your chosen software and the leaf IDs will now be the taxonomic assignments.
  I hope this is useful. Let us know if you encounter any issue or if you would like to do so for a number of files and we could provide you with altered tree files.
  Sincerely, Hubert