suhrig/arriba

About --transcriptSelection option

Closed this issue · 3 comments

emiCbio commented

Thank you for developing such a useful tool.

I have a question about the following section of Arriba's command line options.
https://arriba.readthedocs.io/en/latest/command-line-options/#:~:text=%2D%2DtranscriptSelection%3Dcoverage%7Cprovided%7Ccanonical
At the end of the paragrah, it says that the default for --transcriptSelection is 'provided',
but earlier in the explanation, it seems to say that the default is 'coverage'.
Is my understanding correct that the default is 'provided'?

As far as I investigated, the following modification to the default parameter of "--transcriptSelection" is not reflected in the documentation.
92e09d0

Thanks

suhrig commented

You're right. provided is the default. The documentation needs updating. Thanks for pointing out!

emiCbio commented

I got it. Thanks for your reply!

suhrig commented

Fixed in the develop branch now. Thanks again for reporting.