Mutation rate stats and per base coverage

[aichilizi]

Hi Danny,

Thanks for creating this amazing tool for RNA structure analysis. While I was using this tool, I found it was not very straightforward to generate mutation rate/frequency and per base coverage (shapemapper2 generates automatically) which are important for QC. I think I might be able to get all these info from rc files? But looks like there is no command for rf-rctools -view to make an output files. What would you recommend to do?

Thanks again! Best, JZ

[dincarnato]

Hi JZ,

what information do you exactly look for? Can you show me an example?

The rf-rctools view allows you to get both the mutations per base and the coverage per base on a transcript. Is that the info you are looking for?

Many thanks! Best, Danny

[aichilizi]

Hi Danny, Here is the example. Yes, rc-tools view can get mutations per base and the coverage per base info to calculate these values in the figure. However I can't extract these info from rc-tools view. I think I should ask is there a way to convert the rc file to format that can be viewed on a PC or mac?

Many Thanks! Best, JZ

[dincarnato]

Hi JZ,

I still don't understand. If you do:

rf-rctools view yourfile.rc > yourfile.txt

The output is just a simple text file you can open with any editor.

Danny

[aichilizi]

Hi Danny,

"rf-rctools view yourfile.rc > yourfile.txt". This is what I want! Sorry I am not familiar with UNIX comman-line. Thanks for your help! I will close this issue.

Best, JZ

[dincarnato]

Great! I will make sure to have something similar to those plots generated in future releases.

[aichilizi]

That will be great! Thanks again!