Read Count Analysis (Variant/RNA-Seq)

According to this tool, it is possible to know exactly how many reads matched a given genomic object of the reference sequence for a RNA-Seq or Variant profiling experiment. Results are accessible following a 5 steps process which is described below.

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  • 1. Choose an organism and one or several reference sequences.

  • 2. If several choices are available, you can choose the mapping strategy.

  • 3. If several choices are available, you can choose the exprimental protocol.

  • 4. It is possible to restrict the query to one or several given classes of genomic objects ( CDS, fCDS, rRNA, tRNA, miscRNA or all ).

  • 5. Select at least one experiment and compute the associated read count number per genomic object. (check publication for terminology of experiments, which is displayed in the head of the interface: Sharma et al, 2010, Nature 464:250-255 for the given example)

As usual, results are reported in a table which is composed of 3 main sections (see below).

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  • 1. Export functions. This section allows users to make all genes (or subsets of genes) available for other analysis tools. 3 main operations are possible here:

    • select subsets of genes (by selecting checkboxes on the first column) and export them into a Gene Cart by using the “Export To Gene Cart” button.

    • See one selected gene into the MaGe Genome Browser by clicking on the magnifying glass.

  • 2. The second part reports the main genomic object features : Label (Link to more Genomic Object information), Type, Name, Product, Begin, End, Length, Frame.

  • 3. RNA-Seq Result part : Read count (direct and/or reverse)