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Problems identifying Editing sites in RNA-seq data #5

Open phoman14 opened 5 years ago

phoman14 commented 5 years ago

Hi, I am currently trying to apply your approach to identify potential RNA editing regulation in our own RNA-seq data, however I am having issues generating a list of editing sites.

Could you please provide more details on how you identify RNA_Editing sites using the GIREMI method. I have not been able to reproduce the editing sites identified for ADAR1 that were provided as example data (using the ADAR1 shRNA knockdown dataset taken from ENCODE-ENCSR104OLN). I am currently using the GATK HaplotypeCaller to identify SNPs and filtering the resulting VCF file as detailed in your paper. I then use the VCF and BAMs generated from GATK to run GIREMI. With this current approach I am not able to identify the large reduction of editing sites in the ADAR knockdown samples when compared to control samples

If you could please provide more details on how you identify mutations in the RNA-seq data as well as the how you identify known SNPs before running GIREMI it would be greatly appreciated.

Thank you Philip

giovanniquinones commented 3 years ago

Hi Philip, Sorry for the very, very late response. Only recently I started maintaining the lab's repositories and saw your comment. I feel bad I couldn't back to you on time. If I am still of any help, please let me know! Thanks, Gio