Question: Organism names after Megablast?
1
gravatar for etiennewalex
2.5 years ago by
etiennewalex30
etiennewalex30 wrote:

Hello,

How do I retrieve organism names after MEGABLAST? 2 months ago I was said to use Fetch taxonomic reprentation tool during a Workshop on metagenomic analyzes, but I can't find this tool now.

Thank you!

Etienne

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ADD COMMENTlink written 2.5 years ago by etiennewalex30

Kraken is the new alternative tool, but indexes are pending. More feedback soon (the core team is in a meeting). Thanks, Jen, Galaxy team

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k

Thanks Jen,

I tried to use Kraken but I couldn't because no option is available to select database. I am still with the results of my MEGABLAST with the different GIs, but I am unable to automatically translate these GIs to organism names. Somebody told me to use testgalaxyproject.org and I found the Fetch Taxonomic Represntation tool in the section Old Metagenomics. Is this tool obsolete or why does it not appear in usegalaxy.org? What is the difference between usegalaxy.org and testgalaxyproject.org? I am a little confused. I am now trying to move my different files from usegalaxy.org to the other but I did not find any other option than to download all my files from the first and upload them all to the second, so it is taking a very long time. I am not sure I am doing things as I should do.

Best

etienne

ADD REPLYlink written 2.5 years ago by etiennewalex30

Test is used primarily for testing and is best not used for serious ongoing work. The quota there is also very small compared to Main (10 GB vs 250 GB).

Kraken reference data is pending. https://github.com/galaxyproject/galaxy/issues/1470 https://github.com/galaxyproject/galaxy/issues/1679

I have put in a request to the team to restore Fetch taxonomic groups at least until Kraken is fully functional. I'll include that decision in my final reply here.

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k

Thank you Jen,

I will wait for the restoration of Fetch taxonomic groups. How can I know when it is restored? Do you think it will last a long time?

Thanks !

ADD REPLYlink written 2.5 years ago by etiennewalex30

I would expect this to clear up (Kraken indexes promoted or Fetch Tax restored) sometime this week, but cannot provide a hard timeline. I have this post bookmarked, but please feel free to ask for status Monday if you do not see a resolution and I can provide the latest update. Thanks! Jen

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k

Thank you very much for your help.

Best,

etienne

ADD REPLYlink written 2.5 years ago by etiennewalex30

Dear Jen,

Are this tools available now? If yes, where? I still want to retrieve organism names of my Megablast file.

Best

etienne

ADD REPLYlink written 2.5 years ago by etiennewalex30

Both are still pending: Kraken index migration to main & restoring Fetch Taxonomy to tool panel (if it will be). I asked our development team for an update and will reply if this changes (and adjust the tickets above). Thanks! Jen

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k

Thanks,

Is there another way to automatically get organism names of all my megablast file without these tools?

ADD REPLYlink written 2.5 years ago by etiennewalex30

You can try the test server if you want. The quota is smaller (10 GB) but if just processing the single file you might be OK space-wise. The underlying data is identical to what Main would have (the megablast and taxonomy data are from the same exact builds): https://test.galaxyproject.org/

Alternative options: using other public Galaxy instances, downloading data from NCBI and working with it line-command, etc.

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k

OK thanks for your help!

ADD REPLYlink written 2.5 years ago by etiennewalex30
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