Gencode / Ensembl about armor

[sorjuela]

Hi,

The ARMOR pipeline is a reference-based analysis. We require the specification of Ensembl/Gencode so that the workflow knows how to properly parse the annotation files.

You can read about the difference between these two here: https://www.gencodegenes.org/pages/faq.html . Additionally, Gencode is only for Human and Mouse

In your data, the annotation is not only reference based, but has additional features from the de-novo assembly. We cannot guarantee that the parsing will be done properly, and you might lose information.

You should be able to run the pipeline anyway (or at least try it out). The idea of specifying all the annotation details is to keep track of them. You would have to set the annotation as Ensembl, and your organism as Apis_mellifera. I imagine HAv3.1 is the build, and the version should be in the link you sent, however these shouldn't affect the analysis.

You should also set run_camera as False.

[csoneson]

I'm going to close this issue - feel free to reopen if there are remaining problems.

[ms-gx]

Sorry for no response. I did not get it to run through but did not investigate further.

[csoneson]

Ok. Let us know if we can do something to help (if so, please provide the error message that you get, and check whether the example data set runs through, to see whether it is an explicit problem related to the data, or a more general setup problem).

[ms-gx]

Setup worked fine. The problem was somehow related to the fact that I was not analysing mouse/human data and the format/id or similar was not as expected by your toolchain. Next time I access the system I might quickly report back to you.