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wwood / dirseq

Work out whether RNAseq reads in general agree with the direction of the gene predicted
MIT License
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Option for coverage or counts #2

Closed TYMichaelsen closed 6 years ago

TYMichaelsen commented 6 years ago

Hi Ben, Would it be possible to have a command line option specifying whether to output as coverage or number of reads? Currently it's outputting average coverage, but that is not what i want for downstream analysis.

Thanks for a nice, simple program!

Best Thomas

wwood commented 6 years ago

Hi, Sure, in fact it already does with --measure-type count. This wasn't clear from the README so I've updated it.

Thanks for the kind words. Let me know if there is anything else. ben

TYMichaelsen commented 6 years ago

Awesome, thanks!

TYMichaelsen commented 6 years ago

Hi again Ben,

While you're at it, could you also take a look at the --accepted-feature-types argument? It looks like the argument is set as default CDS by the program, it throws and error when i try to set it myself.

Best, Thomas

wwood commented 6 years ago

Ah, right that option wasn't working. I fixed it just now in the master branch, would you mind testing it? If you are happy I'll release 0.2.1.

If you've already got dirseq installed then I think it should just be a simple matter of running bin/dirseq from the git checkout.

Thanks for the bug report.

ben

TYMichaelsen commented 6 years ago

Great, it works for me now :)

Thanks again

wwood commented 6 years ago

Alrighty, 0.2.1 now pushed.