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vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
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IR documentation #2

Closed timbitz closed 10 years ago

timbitz commented 10 years ago

Output format

mirimia commented 10 years ago

I think this is also done. It's common for the combine format.

Perhaps we want to add a few lines explaining the methods (the binomial test, etc.) but I think referring to the paper (as of now) should be enough.

Thoughts?

UBrau commented 10 years ago

Currently, in the qual scores, score 4 for IR is a composite of read numbers and score 5 the balance p-value. If anyone thinks it's necessary, we could swap these two columns for slightly better consistency. Otherwise, the documentation should be changed to include the following:

Combine output format

Column 8

Score 3

Read coverage, based on uncorrected reads mapping only to the reference C1A, AC2 or C1C2 splice junctions (similar values as per Score 1). Always NA for intron retention events.

Score 4

Imbalance of reads mapping to inclusion splice junctions (only for exon skipping events quantified by the a posteriori or a priori modules; For intron retention events, numbers of reads mapping to the upstream exon-intron junction, downstream intron-exon junction, and exon-exon junction in the format A=B=C) ...

Score 5

Complexity of the event (only for exon skipping events quantified by the a posteriori or a priori modules); For intron retention events, p-value of a binomial test of balance between reads mapping to the upstream and downstream exon-intron junctions, modified by reads mapping to a 200-bp window in the centre of the intron (see Braunschweig et al., 2014). ...