I am using riboSeqR for framshift analysis on ribosome profiling data.
I obtained alignments for individual transcripts using the riboSeqR plotTranscript function. However it is not clear to me how to interpret these plots. Let's take for example Figure 3 at page 5 of the riboSeqR reference manual. Here it is my interpretation, please confirm me if it's correct:
-on the left (nct 1-1039) footprints are mainly in the 0-frame (the plot is colored in red). The second most abundant reading frame is frame 2 (indicated by the horizontal blue line on the top)
-on the right (nct 1477-3667) footprints are mainly in the frame 1 (the plot is colored in green). The second most abundant reading frame is frame 0 (indicated by the horizontal red line on the top)
-in grey is shown the mRNA coverage
-There is a switch from 0-frame to 1-frame: this might be a frameshifting event, right???
Why are there two scales (1 to 150 on the left and 1 to 200 on the right)? Is it on the left the number of reads from footprinting and on the right the right the number of reads from mRNA?