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This is a tool for the visualization of paired-end alignments over a region of genome. For a particular paired-end sample, it allows you to visualize the relationships between the aligned ends using a 2D scattergram indicating the chromosomal positions of the two aligned ends. Each point on the plot corresponds to a paired-end read where both pairs are on the same chromosome but different strands. The <math>x</math>-axis shows the coordinate of the 3’-most base of the plus-strand read, and the <math>y</math>-axis shows the 3’-most base of the minus-strand read. The gray line is <math>y=x</math>, and since the minus strand read is usually downstream, of the plus strand read, most of the points lie near or above the diagonal. In particular, points far from the diagonal usually indicate reads spanning introns, whereas those near the diagonal indicate paired-ends within the same exon. Finally, the color (and size) of the point indicates the number of paired-end reads aligning to those positions.

Pairplot options
Set The project for which you want to examine paired-end distributions. Only paired-end RNA-Seq projects will appear in this list.
Group The sample for which you want to generate a pairplot.
Region The chromosomal region you would like to examine, in the form $chr:$start-$end (for example, "chr1:10995265-11008136").
Highlight Pairplot-Highlight
Width {{:2way-width}
Height {{:2way-height}