Images not created for GRCh37

Question

Images not created for GRCh37

rhshah opened this issue 8 years ago · comments

Hi There,

Great tool, I am trying to make plots for GRCh37 and i only get is the *1_cdna.fa, none of the other files and images get created.

This is the command that i run:
agfusion --gene5prime ENSG00000197157 --gene3prime ENSG00000157764 --junction5prime 127389835 --junction3prime 140490224 --genome GRCh37 --out SND1-BRAF

I am able to replicate you example for mouse genome.

Thank you for your help in advance.

Best,
Ronak

Charlie Murphy · Answer 1 · Wed Oct 19 2016 10:33:34 GMT+0800 (China Standard Time)

Ronak,

Thanks for trying out AGFusion. It appears there is a bug where it does not properly handle fusion junctions in introns. I patched the code, so reinstall from here or pip and let me know if it works for you.

Ronak Shah · Answer 2 · Thu Oct 20 2016 00:34:28 GMT+0800 (China Standard Time)

Thank you for your prompt response, it does work now.
Currently you only support Ensembl Id, are you planning to RefSeq Id ?

Charlie Murphy · Answer 3 · Thu Oct 20 2016 00:36:16 GMT+0800 (China Standard Time)

Yes, supporting RefSeq Ids is on my list of features I want to add.