Metagene Analysis (version 0.4.0)

Select Triplet periodicity (R data file):

filterHits parameters (footprint reads to be used in the analysis)

Length of ribosome footprint reads to be used in filtering (lengths):

ex: 27,28. Multiple values must be comma-separated. Please consult Periodicity-report.txt.

Frames of the ribosome footprint reads to be used in filtering (frames):

ex: 1,0. Should be of equal length to the lengths parameter above. Multiple values must be comma-separated. Please consult the periodicity report from previous step.

Mean number of hits within a replicate group that should be observed to pass filtering (hitMean):

Mean number of unique sequences within a replicate group that should be observed to pass filtering (unqhitMean):

Check the ratios of the expected phase to maximal phase within the putative coding sequence (ratioCheck):

plotCDS parameters

Length of footprints to be plotted (lengths):

Multiple values should be comma-separated. In that case, multiple plots will be produced

The distance upstream of the translation start to be plotted (min5p):

The distance downstream of the translation start to be plotted (max5p):

The distance upstream of the translation end to be plotted (min3p):

The distance downtream of the translation end to be plotted (max3p):

If given, caps the height of plotted values (cap):

Title of the plot (main):

About

Metagene analysis using riboSeqR. The input is the R data file from the previous step - Triplet periodicity.

riboSeqR version: 1.0.4.

How to use?

Inputs

Select Triplet periodicity (R data file) from the previous step.
Specify length of ribosome footprint reads to be used in filtering (lengths). Only these reads will be used in the analysis.
Specify frames to consider. This information can be obtained from the Triplet periodicity (HTML report).

Please note that the frames specified should correspond to the lengths of the reads.
Under plotCDS parameters, input length of footprints to be considered for generating the plot.
Review/change other options if necessary and execute program.

Outputs

The following files will be generated on completion:

Metagene analysis (HTML report)

A HTML file with results and links to other output files - plots for specified lengths (PDF) and R script used for the session.
Metagene analysis (R data file)

Used as input for the next step - Plot Rribosome Profile.

riboSeqR functions used

filterHits.

For detailed description of the functions and the options used, please consult the riboSeqR documentation.