brianjohnhaas
commented
2 years ago hi,
responses below
On Mon, Jan 17, 2022 at 3:06 AM Konstantinos Kyriakidis < @.***> wrote:
Hi @brianjohnhaas https://github.com/brianjohnhaas
Q1: I want to use ctat-mutations to find RNA Editing events. I have only RNA Seq data. Does your implementation find most of the variants around all genomic regions or does it have a preference for variants in specific regions of the genome (e.g. coding). I am telling this because my data have high intron mapping for some reason.
it doesn't restrict to specific genomic regions
Q2: Should I use a boosting method for my use case? If yes, which one do you propose?
The default 'xgboost' tends to work the best.
Q3: Is it in your plan to update REDIportal to V2?
we will plan to update rediportal later this year for the next release. It requires that we redo our benchmarking and testing.
best of luck!
Thanks!
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
kokyriakidis
Hi @brianjohnhaas
Q1: I want to use ctat-mutations to find RNA Editing events. I have only RNA Seq data. Does your implementation find most of the variants around all genomic regions or does it have a preference for variants in specific regions of the genome (e.g. coding). I am telling this because my data have high intron mapping for some reason.
Q2: Should I use a boosting method for my use case? If yes, which one do you propose? I saw in your code that it removes RNAEditing column when it prepares for boosting. Does that mean that the variants that are annotated with RNAEDIT will not be in the final vcf file? And this vcf file will likely not contain other RNAEditing events because they will be filtered by the model? Do you think that boosting will likely remove potential RNAEditing events from the vcf because they will be considered as FPs?
Q3: Let's say I do not use boosting. Do you thing HC hard filters will likely remove potential RNAEditing sites from the vcf because they will be considered as FPs by the filters?
Q4: Is it in your plan to update REDIportal to V2?
Thanks!