updated main README and MenT1 notebook

README.md

@@ -6,8 +6,27 @@
 
 The EMOTE-tk R library focuses on exact 5'-end and/or 3'-end quantification of RNAs *via* targeted RNA-Seq.
 
+![Overview schema of the features provided by the EMOTE-tk R library regrouped by
+phases of an RNA-end sequencing project.](img/EMOTE-tk.library.topics.png)\  
+**Figure 1: Overview schema of the features provided by the EMOTE-tk R library regrouped by
+phases of an RNA-end sequencing project.** EMOTE-tk provides functions (A) for FASTQ reads pre-
+processing, manipulation and validation based on a read_features table describing the structure of
+sequencing reads; (B) for aligning reads on reference sequences and compute abundances at the
+single nucleotide resolution to obtain (C) a count table representing the abundances (count) of RNA
+3' or 5' ends mapped to a reference sequence (rname) at a certain location (position) on a strand. In
+this example, the reads contain UMI extracted in the pre-processing step that are used at this step
+to remove PCR amplification duplicates introduced in the library preparation. (D) the count table
+can be further manipulated to apply some normalization or filtering to prepare the downstream
+analyses. (E) EMOTE-tk provides functions for downstream analysis of the count table for TSS
+identification, analysis of RNA-ends species proportions (e.g. 5'P/5’PPP in WT vs. mutant strain),
+periodic signal analysis such as ribosome translation speed profiling, or the exploration of 3' end
+modifications. (F) EMOTE-tk count table can also be analyzed further by other libraries: we illustrate
+this by a differential expression analysis to identify endoribonucleolytic cleavage sites by comparing
+abundances between WT and endoRNase deletion mutant strains.
+
 Features:
-* Pre-processing raw reads fastq file 
+
+* [Pre-processing raw reads fastq file](scripts/Pre-processing.ipynb)
   * Reads parsing and validation
   * Reads feature extraction
   * Demultiplexing into separate fastq files
@@ -22,6 +41,7 @@ Features:
   * Differential proportion statistical analysis
 
 Applications:
+
 * TSS identification → [notebook](scripts/TSS.identification.Prados-2016.ipynb)
 * Endoribonucleolytic cleavage sites identification → [notebook](scripts/Endoribonucleolytic.cleavage.sites.identification.Broglia-2020.ipynb)
 * co-translational degradation → [notebook](scripts/Co-translational.exoribonucleolytic.degradation.Khemici-2015.ipynb)