search

bioinfo-biols / CIRIquant

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

quantification and differential expression analysis for RNase R treated samples #4

Closed cuijr1995 closed 4 years ago

cuijr1995 commented 4 years ago

Hi kevin, I'm not very clear the steps of "Generate RNase R effect corrected BSJ information" . Should I run CIRIquant with RNase R treated samples 2 times and add --RNaseR option with "the output gtf of the first time" on the second time? Moreover, how cao I do the differential expression analysis for RNase R treated samples? I'd appreciate it if you could give me some advice. Thanks!

Kevinzjy commented 4 years ago

In order to remove RNase R effect, you need to have two paired samples (1 untreated + 1 RNase R treated), and use following steps.

  1. Run CIRIquant with RNase R treated sample
  2. Specific the output RNase R treated GTF using --RNase R option when runnning CIRIquant with the untreated data.

Then, CIRIquant will generate the corrected expression values of circRNAs detected in your RNase R treated sample.

For differential expression analysis, you can use CIRI_DE command using output gtf after RNase R correction:

CIRI_DE -n control_corrected.gtf -c case_corrected.gtf -o CIRI_DE_corrected.csv
cuijr1995 commented 4 years ago

Thanks very much!