Closed xiongxxp closed 4 years ago
Hi, thanks. I'll check it out and let you know. Can you also show me experiment.txt?
Simona
Hi Simona, Thank you for your prompt reply. Here is the screenshot for experiment.txt.
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.
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
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
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
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
screen shot. Thank you for your help.