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bioinfo-biols / CIRIquant

circular RNA quantification tools
https://sourceforge.net/projects/ciri/files/CIRIquant
MIT License
27 stars 18 forks source link

More Precise Definition of Options #7

Closed DarioS closed 4 years ago

DarioS commented 4 years ago

I was reading the user guide and I saw that --tool is described as "User provided tool name for circRNA prediction" and I was wondering if this was any name the user would like to use to refer to the tool or if there are a limited set of valid values. I found the answer to my uncertainty by reading the source code and noticing:

TOOLS = ['CIRI2']
if tool not in TOOLS:

This information should be in the user guide and any other parameter which has a restricted set of allowed values should show all of the allowed values in the user guide. I also wonder if there could be a vignette showing the use of CIRI2, CIRIquant and CIRI-vis, to show users a full end-to-end workflow. For example, maftools has a nice vignette showing all of its major features using a built-in AML data set.

Kevinzjy commented 4 years ago

Thanks for the advice, I'm planning to add support for circRNAs predicted from other widely used tools: e.g. CIRCexplorer2 / find_circ / KNIFE, and I will update detailed information about --circ and --tool in the same time.

DarioS commented 4 years ago

--circ and --tool are optional. Is there any benefit to running CIRI2 first, or should I save time and start from CIRIquant? I notice that CIRIquant has the same input as CIRI2 - a pair of trimmed reads files. Is running CIRI2 before CIRIquant recommended or does CIRIquant completely replace CIRI2?

Also, I noticed a typing mistake; -o, -out should be -o, --out (two dashes for word) in README file.

Kevinzjy commented 4 years ago

CIRIquant include a copy of CIRI2 program to predict circRNAs when --circ and --tool options are not provided, so you won't need to manually run CIRI2 anymore.