Question: Custom gene annotations for SGSeq
0
gravatar for 116100016
16 days ago by
1161000160
1161000160 wrote:

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?

ADD COMMENTlink modified 16 days ago by Leonard Goldstein110 • written 16 days ago by 1161000160
Answer: Custom gene annotations for SGSeq
2
gravatar for Leonard Goldstein
16 days ago by
United States
Leonard Goldstein110 wrote:

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.

ADD COMMENTlink written 16 days ago by Leonard Goldstein110

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?

ADD REPLYlink written 16 days ago by 1161000160
1

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)
ADD REPLYlink written 16 days ago by Leonard Goldstein110
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