How to handle SHAPE-MaP Replicates #39
Description
Our lab was recently discussing how to deal with replicate SHAPE-MaP data. Is there an accepted convention? Does RNAvigate has tools to handle replicate SHAPE-MaP data?
For any given experiment, we routinely perform replicates for SHAPE-MaP samples. For examples, if we were performing SHAPE-MaP on an RNA probed in cells, we would probe cells separately on two different days, process the RNA separately, and sequence them on the same Illumina chip (separate samples, so we get separate .fastq files back for each replicate).
We normally average the Norm_profile column in the x_profiles.txt and map the nucleotide average Norm_profile onto the RNA secondary structure.
Any help would be appreciated!