Codon_density (version 1.0.0)

Reference annotation file (GFF):

Replicate option:

First replicate of first condition (Bam file):

Second replicate of first condition (Bam file):

First replicate of second condition (Bam file):

Please choose a ribosomal site for codon analysis:

Off-set from the 5'end of the footprint to the A-site:

Lenght of the best phasing footprints:

Condition one:

Required even if no replicate

Condition two:

Required even if no replicate

Color for first condition:

Enter standard name, hex color string, or rgb code. You can find all colors here : http://pythonhosted.org/ete2/reference/reference_svgcolors.html

Color for second condition:

Enter standard name, hex color string, or rgb code. You can find all colors here : http://pythonhosted.org/ete2/reference/reference_svgcolors.html

Summary

This tool uses Ribo-seq (BAM file) to determine whether codon occupancy differs between two sets of conditions. For each footprint, the codons at the chosen site are recorded and a histogram displaying all the normalised codon numbers is plotted for both sets of conditions. A second histogram groups together all the codons corresponding to a given amino acid. A chi-squared test is then carried out to determine whether the distribution of the codons used is the same in both sets of conditions.

Output

This tool provides an html file containing graphs and a statistical test result. An additional csv file with codon numbers is provided.

Dependances

This tool depends on Python (>=2.7) and following packages : numpy 1.8.0, Biopython 1.58, scipy 0.12.0 and matplotlib 1.3.1. Samtools is used for bam manipulation.