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Aufiero / circRNAprofiler

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(!): .txt file reported in experiment.txt is not present in folder #3

Closed xiongxxp closed 4 years ago

xiongxxp commented 4 years ago

Hi Simona, Nice circular RNA study tool. I tried the package today. When I enter the command "check <- checkProjectFolder()", there is an error. It says " .txt file reported in experiment.txt is not present in folder named circexplorer2". But I did put all cicRNAs__X.txt files in the folder. I don't know why the program still couldn't locate them. Please refer to the

circRNAprofiler

screen shot. Thank you for your help.

Aufiero commented 4 years ago

Hi, thanks. I'll check it out and let you know. Can you also show me experiment.txt?

Simona

xiongxxp commented 4 years ago

Hi Simona, Thank you for your prompt reply. Here is the screenshot for experiment.txt.

experiment

I guess it's the directory problem. If I use setwd("d:/projectCirc") as directory. Then it shows ".txt file reported in experiment.txt is not present in folder named circexplorer2". But if I use setwd("d:/projectCirc/circexplorer2") as the directory, the error is missing gtf file & experiment.txt is absent or empty, and the program was able to locate those cicRNAs__X.txt files. I assume d:/projectCirc is the main working directory. Thank you.

Aufiero commented 4 years ago

Hi, projectCirc needs to be set as your working directory. I think the problem is in experiment.txt, you missed the .txt in your file names, you only wrote circRNAs_0.37, it has to be circRNAs_0.37.txt, circRNAs_0.38.txt etc

Let me know when you correct if it works.

S

xiongxxp commented 4 years ago

Hi Simona, Yes, you are right. I missed .txt in the experiment.txt. file. Now it works. Besides, do I still need to run mergeBSJunctions() command since I have only one circRNA detection tool (circexplorer2). And the manual is for multiple detection tools. How do I modify accordingly based on only 1 tool (not sure about the step of mergeBSJunctions() and filterCirc())? Thank you. Best, XP

Aufiero commented 4 years ago

Hi,

You can run mergeBSJunctions() also if you used only 1 circRNA detection tool, or in this case you can also skip this step and use directly the backSplicedJunctions dataframe generated by getBackSplicedJunctions() for the downstream steps, e.g.:

filteredCirc <- filterCirc(backSplicedJunctions, allSamples = FALSE, min = 5).

I'll will specify that in the vignettes so that it is clearer.

Best, S