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Just wondering what people's thoughts are on making a standalone tutorial for splicing?
e.g. making a training module out of the DEXSeq part that used to be part of the reference-based tutorial her…
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Question 1
In my case of using rMATs. Too many MXE events in >80% samples (see attached). I also found most differentially expressed splicing events were MXE. Did these reasonable?
[AS_sample_number…
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Hello David,
Is there a way to model individual as random effect as part of the differential splicing analysis, so that one could account for non-independent samples (duplicates) or repeated measurem…
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Dear SUPPA2 Development Team,
I am in the process of using SUPPA2 for differential splicing analysis and have encountered an issue with batch effects in my dataset, which includes sequencing sample…
XXuxi updated
8 months ago
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Hi,
I am using single end library for my differential splicing analysis. As I use regtools (version 0.5.2, -s 2) to generate junc files it recognize junctions on one strand and not the other. There…
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Hi, thanks for developing leafcutter!
I'm trying to understand the impact of the option -p in the intron clustering step regarding the generation of "\*_refined" from "\*_pooled" (using leafcutter_…
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Hi @goldenflaw,
I've prepared an RData file from my differential splicing analysis run using data aligned to the hg38 reference genome from the UCSC hg38 reference genome download page using HISAT2…
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Hi,
I have about 30 samples which I want to do a differential splicing analysis on.
The instructions for including unannotated splice sites suggests that I first merge all my bams into a sing…
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Hi,
I had a few quick questions about how I should interpret the "Samples ()" columns in my results file. Do these columns just refer to how many samples contained the splicing event in the SJ.out.…
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Hello ,
I am performing differential splicing analysis on mouse RNA-Seq following [this](https://davidaknowles.github.io/leafcutter/articles/Usage.html).
I can not run leafcutter R installation ste…