Fig. 1
From: ISVASE: identification of sequence variant associated with splicing event using RNA-seq data
Schematic diagram of the ISVASE software. a Identify splicing variants in RNA-seq data. All splicing variants can be divided into four types according to relationship between target splicing variant (red colour) and other splicing variants (from left to right): (i) unique splicing variant; (ii) splicing variants with same junction start; (iii) splicing variants with same junction end; and (iv) splicing variants with same junction start or end. b Identify sequence variants for each splicing variant and all related splicing variants. To handle all splicing variant types, we identify sequence variants for two parts of splicing separately. In the left part, for junctions with orange, yellow and red colour, the all related splicing variants should be three (all these junctions); however, for junctions with green and blue colour, the total junction is one (itself). Similarly, in the right part, junctions with red, green and blue colour have three all related splicing variants while junctions with orange and yellow colour only has one related junction (itself). c Identify associations. This step includes three significant judgements for sequence variants, junction existence and association between sequence variants and junctions, respectively. The example shown two junctions with same junction end. For junction one (top), two sequence variants are identified (left G(ref)- > C(alt) and right G(ref)- > A(alt)). In sequence variant significant judgement, left is filtered (p value = 1) while right passes the test (p value = 0.0476). In junction significant judgement and association judgement, p value of top junction is 0.0128 (significant) and 0.0070 (significant) respectively. Dashed lines represent gaps in the alignment