Hello everyone! Which appliance on Galaxy would you recomend for Eukaryotic genomic annotation? It would be even more helpful if there was one capable of intersecting or cross-linking information from two or more Exomes. The Galaxy tutorials used GEMINI and Funannotate but those appear to no longer be availiable.
Thank you in advance, Anna
hi @Anna
the GTN tutorials has information about compatibility(?0 with popular Galaxy servers. For example, both Gemini and Funannotate are available at usegalaxy.eu. It is OK to have account on different Galaxy servers. Data can be moved directly between Galaxy servers: click at Copy Link (chain) icon at the dataset to be copied, and paste the link into Upload menu on the target Galaxy server, into Paste/Fetch Data tab.
What do you mean by cross-linking information from two or more exomes? Do you mean something like multi-sample VCF file?
Kind regards,
Igor
Hey @igor! Thank you again for all the help!
I have two VCFs, one from a normal blood sample and one from diseased tissue from the same patient (not tumor, so standard cancer gene tools may not be helpfull). I´d like to compare them for somatic mutations only on the diseased tissue and possible loss of heterozigosity. I was able to generate a VCF of the differences between the two with VCF-VCF intersect as you suggested and I have annotated both of the VCFs with VEP but can seem to annotate the “intersected” VCF, the error message states “the index file is older than the data file”. I was planning to use GEMINI to read them.
Hi @Anna
I believe if you intersect annotated VCF files, the output file will have the annotations present in the input file(s).
Galaxy servers usually have several intersection tools. Maybe try different tools.
Kind regards,
Igor
1 Like
Worked out perfectly, thank you again for all of the help, @igor !
Anna
1 Like