Annotating Gene IDs -local-DESEQ2 rats AnnotateMyIDs

RichardBJ · May 19, 2019, 4:01pm

Hi there, I have seen several posts pertaining to annotation of the DESEQ2 output GeneID with gene name (ENSRNOG00000046834 etc) and for mice and humans it works easily with the AnnotateMyIDs tool. I work with rat tissue. I have installed this AnnotateMyIDs on our server, but it does not support rats. I have tried to fiddle with the code to get it to accept rats too, but have failed so far and am worried about stuffing the server!
Is there a way to add rat support to this, as admin? IF not is it possible to make a feature request somewhere for this? …It was developed by IUC. I don’t know who that is. I ran Uniprot mapping and this gives a list of the converted gene names, but not in the same file (unless I did it wrong). Is there an easier way? Thanks.

I have written a program to do this in Python outside of Galaxy. Be nice to all be inside though!

RichardBJ · May 20, 2019, 8:11am

Found a way to do this around the houses; uniprot ID mapping (creating a standalone dataset) followed by “find in reference” tool, followed by some text clean-up. Would still be brilliant if annotateMYIDs would do rats though.

bjoern.gruening · May 20, 2019, 12:25pm

I think this is possible, it just means that we need to store and download another GB of annotation. I will look at this asap, promised.

RichardBJ · June 4, 2019, 9:40am

…thanks…
BW
R.

bjoern.gruening · June 5, 2019, 4:15pm

@RichardBJ can you try it for me please?

RichardBJ · June 6, 2019, 9:52am

@bjoern.gruening …sorry, try what/which? Did you alter annotateMYids? The Galaxy ToolSched AnnotateMYids does seem to have updated (for my installation) and when I tried annotatemyids on usegalaxy.org it still just has humanoids, mice, flies and zebras… I am assuming I have missed something… sorry…

jennaj · June 6, 2019, 9:55am

Try it at the Galaxy EU https://usegalaxy.eu server.

If it works there, then the other usegalaxy.* servers will be updated as well.

RichardBJ · June 7, 2019, 12:37pm

Ah! EU Galaxy
Yes, so I created an account there, uploaded a rat DESEQ2 and it worked beautifully.
If you do update on other Galaxies, any chance you could pop up simple instructions for setting that up through our local installations too?
Thank you guys so much!!!

RichardBJ · June 16, 2019, 8:26am

@bjoern.gruening thanks, so yes that did work. Is it possible to install this tool on our own installations?

jennaj · June 20, 2019, 7:53pm

@RichardBJ, @bjoern.gruening will see your reply and give instructions.

The tool itself has not been updated yet to include Rat for use in a local Galaxy. He was probably waiting for your feedback first, then is finding time to update the tool itself so everyone can update (public + local).

Repository: https://toolshed.g2.bx.psu.edu/view/iuc/annotatemyids/ecc913a7334b

jennaj · June 20, 2019, 8:01pm

Update: I also ping’d the IUC (tool authors) to see if they can offer more help/advice soon-ish. Feel free to join in on the conversation: https://gitter.im/galaxy-iuc/iuc?at=5d0be4c91e35ef14b687c982

mblue9 · June 21, 2019, 12:44am

I’ve added rat to annotatemyids and submitted a PR to the IUC repo here, let’s see if it’s accepted https://github.com/galaxyproject/tools-iuc/pull/2462

By the way there is also this deg_annotate tool that can annotate deseq2 output with a GTF so maybe that’s another option? https://toolshed.g2.bx.psu.edu/repository?repository_id=e33c4ee81be2b1b4

RichardBJ · June 28, 2019, 8:23am

Thanks so much, hopefully it will be available to install soon. I have never managed to get deg_annotate to work. No idea why!! No errors, just whether I use GTF or GFF3 I get columns of NA. Tried all flavours of keyword options in addition to the defaults…

mblue9 · June 28, 2019, 9:55am

It’s already available to install, it’s this version here https://toolshed.g2.bx.psu.edu/repository?repository_id=c8658b82d8429f5d&changeset_revision=1aae04680c4b

That’s a shame deg_annotate didn’t work for you, do you have a history that you could share?

RichardBJ · July 14, 2019, 8:50am

Thank you!! So I immediately deployed this on my server and it works well. Sorry for the delay in reply though!!
As for reg_annotate not working for me; when you say “history to share” do you mean that literally?.. I am not sure I know how to share a history on this forum. If you mean just describe what happens and what goes wrong, of course I can do that, but I think it is my fault not a bug?
Thanks again.

jennaj · July 15, 2019, 11:47pm

The FAQ for how to generate a history share link: https://galaxyproject.org/support/

Sharing and Publishing your work

Warning: if this is on your own server and it is not hosted publically, others won’t be able to access the share link.

What happens if you run this at Galaxy EU https://usegalaxy.org? Same error or different or successful? If an error, a share link to the history could be generated and posted back. Either publically in this post or with @mblue9 in a direct message (click into your account in the upper top right corner then immediately under find the “letter icon”).