Closed ahdee closed 5 years ago
Hi @ahdee! I'm not able to look at this right now but could you also share your SOAPFuse results file? Then I can look at both and compare when I have the time :)
Hi @ahdee and @stianlagstad, I encountered the same problem, and fyi I think the problem is with the ensembl ids as generated by STAR-Fusion which includes the version numbers (following the period). Stripping the version number manually seems to work.
Thank you very much, @sraorao!:) @ahdee please let us know whether this works for you. If it does, I can modify the import function for STAR-Fusion to strip the version number.
Yes it works! Had to manually delete the ENS...\.+
Thank you very much, @ahdee and @sraorao. I've fixed the parsing of the Starfusion ensembl id, but unfortunately not in time to update the Bioconductor 3.7 release. You can however get the fix by cloning the 3.7 branch from GitHub: https://github.com/stianlagstad/chimeraviz/tree/RELEASE_3_7.
The fix will be present in the upcoming 3.8 release :)
3.7 fix: https://github.com/stianlagstad/chimeraviz/pull/50 3.8 fix: https://github.com/stianlagstad/chimeraviz/pull/49
Hi, I'm using STAR-Fusion-v1.3.2 and the chimeraviz: "1.6.0". I was able to input the tsv file from star-fusion and circos plot can be generated. However, when I tried
I get this error.
When I the same fusion and sample is imported with soap the code runs perfectly.
I included a test tsvfrom Star. ( file name is .txt so that I can upload example)
thanks!
test.txt