Closed alexjfortuna closed 5 years ago
Hi @alexjfortuna ,
What annotations set are you using for star-fusion? Can you give me more details on the fusion? what are the breakpoints/strand for it?
Also which annotation files did you run mavis with?
Hello @creisle I am using the annotations for hg19 which came from MAVIS. These are ensembl69 IDs. When I click on the file I do not see C11orf95 as an annotation.
For Star-Fusion I am using the annotations that come with the package. They are Hugo IDs.
I have attached the MAVIS summary file here which includes the breakpoints for the RELA Fusion, which is the one I am concerned about. mavis_summary_XXX.txt
@alexjfortuna by default we included only the protein-coding genes/transcripts in the default annotations file. Ensembl doesn't host the archive for 69 anymore, but the closest related archive 67 has this with no protein-coding transcripts. http://may2012.archive.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000188070;r=11:63527364-63536113
It should be pretty straightforward to build a reference file including non-coding genes. We still have the copy of the 69 db locally. Would that be helpful?
Hi @creisle if you could build a reference for us which includes non-coding genes that would be most helpful!
Hi @creisle is this ready to test?
@alexjfortuna we have generated the new annotations file. We are just running it with some test libraries on our end to profile if it will change the memory/time requirements and if so by how much. We should have something ready for you to test in the next couple of days. Thanks for being so patient
Hi @alexjfortuna we have generated the annotations file see http://mavis.bcgsc.ca/docs/latest/mavis_input.html#annotations for the link to the new file.
This file is quite a big larger so it will require more memory by default for the annotation step (see the warning next to the link)
We also added a fix to ensure that the loading does not break on the JSON containing number vs string for the strand.
Please test with the latest release 2.2.5
I have installed the latest release 2.2.5 and am running with the larger annotation file. Will report back. Thank you so much!
Working well! Thank you for all the help
MAVIS version: <2.2.1>
Python version: <3.6.4>
OS: <ubuntu 18.04>
Expected Behaviour
I would like to receive annotated fusions; I view the fusion I am expecting; however instead of gene1 = C11orf95; the gene1 says None. Can I update the gene annotations?
Actual Behaviour
Genes annotated in a similar manner to star-fusion, which is the input file in this case.
Steps to Reproduce the Behaviour