Comparative study of reliability and sensitivity of the current mapping software used for the analysis of NGS data (RNA-seq paired-end)

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1. IBC AXE1
Supervisors: David Piquemal and Laurent Manchon

Comparative study of reliability and sensitivity of the current mapping software used for the analysis of NGS data (RNA-seq paired-end)

The application of next-generation sequencing technology to gene expression quantification analysis, namely, RNA-Sequencing, has transformed the way in which gene expression studies are conducted and analyzed. These advances are of particular interest to researchers studying organisms with missing or incomplete genomes, as the need for knowledge of sequence information is overcome. Mapping assembly methods have gained widespread acceptance in the RNA-Seq community for organisms with reference genome. While such methods have tremendous utility, computational cost is still a significant challenge for organisms with large and complex genomes.
For each of these methods, we need to explore mapping rates and locations, number of detected genes, correlations between computed expression values, and the utility of the resulting data for differential expression analysis.
Reference-based alignment methods utilize the sequence for each read (and it's mate in paired-end data) to find potential mapping locations by exact match or scoring sequence similarity. Mapping locations indicate transcripts of origin, and the number of reads originating from a given transcript inform on how much of the transcript was present in the sample.
To compare the reference-based mapping methods and report correlations between them we need to examine several mapping approaches as for example using first the default parameters for each tool.
Then to improve mapping scores, all of the reporting parameters of these mapping tools may be adjusted.

Required skills: Computer programming skills, algorithms, knowledge of biology

CV and motivation letter should be sent to : David Piquemal <This email address is being protected from spambots. You need JavaScript enabled to view it.>