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.
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).
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:
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)