Custom gene annotations for SGSeq
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116100016 • 0
@116100016-22156
Last seen 22 months ago

I tried using the do novo splice prediction to see if it could detect other splice variants in the androgen receptor. Though it correctly identified the exons, it couldn't identify any of the splice variants in the annotated file. So I was wondering if it is possible to input a custom annotation, or in my case, just add a few more junctions to cover the newly added AR variants from the literature?

sgseq alternative splicing rna seq • 255 views
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@leonard-goldstein-6845
Last seen 12 months ago
United States

Yes you can work with a combination of annotated and predicted gene models. The easiest way to do this is to use analyzeFeatures() for annotated gene models as explained in the vignette but with predict = TRUE.

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What if instead of de novo prediction I just want to add a few hg19 junction coordinates (i.e. [66950000, 66953200]) to the Features object? Is there a way to just add a few in?

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You can add junctions manually for a TxFeatures object. But you have to be careful that coordinates are consistent with exons. Junction starts and ends have to coincide with exon ends and start, respectively. Here is an example for TxFeatures object txf_ann that comes with the package:

new_junction <- TxFeatures(GRanges("16:87365116-87368910:-", type = "J"))
new_txf <- c(txf_ann, new_junction)
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