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suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data
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How to get the exon number from output? #168

Closed bbgbb closed 2 years ago

bbgbb commented 2 years ago

Hi,

I want to check the exon number of the fusion gene but i don't find how to... What command should I use to get the exon number?

Thanks!

suhrig commented 2 years ago

Hi,

The exon numbers are shown in the PDF file generated by draw_fusions.R. Or do you need them in a machine-readable format?

Regards, Sebastian

bbgbb commented 2 years ago

Hi @suhrig ,

Thanks for your reply! I saw the exon numbers can be shown in PDF file. And I wonder whether them can be in format like dataframe (csv or txt)?

Thanks

suhrig commented 2 years ago

Here is a script which appends two columns with the exon numbers to Arriba's output files: annotate_exon_numbers.sh.zip. Run it without arguments to learn about the usage.

Let me know if you have trouble using it. I tested it on a few files and it seemed to work fine.

bbgbb commented 2 years ago

Hi Sebastian @suhrig ,

The script is super helpful! Thanks a lot for your help! Hope you have a nice day.=)

Thanks again.