riboSeqR: interpret plots generated by plotTranscript function
0
0
Entering edit mode
@laurafancello-6772
Last seen 9.9 years ago
Belgium

Hi,

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?

Thanks!

Laura

riboSeqR plotTranscript function • 1.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 756 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6