bPeaks explorer

bPeaks exmplorer allows the exploration of bPeaks analyzer results.The page is divided into 5 parts :

Import area

3 files can be imported:

a zipped file obtained with Bpeask (Data folder)
an annotation file in gff or gff.gz format. It is possible to find this type of file on NCBI genome. An example file is available on Github (Data folder)
An annotation file to fill the database. This file is composed of 8 columns: the feature name, the database name, the standard name, the beginning and end position of the gene, the chromosome, a description and the organism. The file is in TSV format (separator : tabulation). A example is available in Github (Database folder)

The summary area is divided into 4 parts:

The genome viewer offers a dynamic exploration of the results. It is composeb by two graphs :

Number of read mapped according to genomic position
Annotations of peaks (gray) and genes (orange for strand + and purple for strand -). Click on extremity

Two types of additional information can be displayed in this field:

if you click on an extremity of gene (orange or purple segment) (if a gff is imported) :
- The informations present for this gene in the database
- The informations present for this gene in the gff
if you click on an extremity of peak (gray segment) :
- A set of information about the peak such as its position, chromosome and sequence if a fasta file with the reference genome was used in the analysis.
- A pdf with for this peak a graph of T1, T2 T3 and T4

For each chromosome, you will find in this zone 6 graphs :

A average number of reads in peak detected in comparison with all chromosomes (boxplots)
A average of logFC in comparison with all chromosomes (boxplots)
A average of quantile in comparison with all chromosomes (boxplots)
Lorenz curves
IP sample PBC according to Ip sample PBC
Number of positions (logged) with a given number of reads