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SplAdder:v2.4.2
chenqingwang 4 år sedan 23 ändringar mot master sedan detta släpp
SplAdder is a heuristic
We would like to reiterate here that SplAdder is a heuristic approach, that employs a system of empirical filter rules on RNA-Seq data to extend a splicing graph pre-defined by a given annotation. Due to this heuristic nature, there is a list of things one should keep in mind when working with the software:
Although the algorithm is deterministic, it is sensitive to the order of input data. Especially when you are working with many input samples and integrate their information to generate a single splicing graph, the order of input files might influence the outcome. However, in most cases the generated splicing graphs are robust against changes of the order of the input.
Depending on the annotation file that you are using, some annotated gene regions might be subject to filtering. SplAdder will automatically ignore all introns in the input data that could be assigned to more than one gene in the annotation. (This decision is strand-specific, that is both genes and the intron need to be on the same strand.)
As SplAdder will sample all possible events from the graph, there can be a certain redundancy in the events (although all events are unique as a whole). For instance, if there are 3 possible donors paired with an acceptor in a gene on the positive strand, SplAdder will output all three possible pairs of alternative 3 prime splice site events.
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