Not able to see protein domain information

[Nitin123-4]

Hi,

I am trying the below command and I am not able to see any Protein domain information for GRCh37.

agfusion --gene5prime ENSG00000140464 --gene3prime ENSG00000131759 --junction5prime 74325755 --junction3prime 38504568 --genome GRCh37 --out PML-RARA

Please help me regarding this.

[Charlie Murphy]

Apologies, yes this is an issue I'am aware of. The reason is I acquire the protein domain information directly from the Ensembl MySQL database. And protein domain information is available for GRCm38, but not GRCm37. So I need to find a way around this. Will try to fix this today

[Nitin123-4]

Hi, Thank you for your kind reply. I am working in GRCh37. Thank you Regards

…

On 20 April 2017 at 22:09, Charles Murphy ***@***.***> wrote: Apologies, yes this is an issue I'am aware of. The reason is I acquire the protein domain information directly from the Ensembl MySQL database. And protein domain information is available for GRCm38, but not GRCm37. So I need to find a way around this. Will try to fix this today — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYo9GQ8anw4xtLgibyTBUZkW8lSYMM3Dks5rx4o2gaJpZM4NDQ1l> .

-- Nitin Mandloi Senior Bioinformatics Analyst MedGenome Labs Pvt. Ltd. Bangalore *INDIA* *Think Green* Mobile no: [phone], [phone]

[Charlie Murphy]

Should be fixed now, reinstall from pip or from GitHub. Also be sure to add "annotate" to the command call (I' am doing some code reorganization).

agfusion annotate --gene5prime ENSG00000140464 --gene3prime ENSG00000131759 --junction5prime 74325755 --junction3prime 38504568 --genome GRCh37 --out PML-RARA