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Hello everyone,
I'm encountering an issue while running a Baltica workflow (version 1.2.4, python 3.7.12) with unstranded RNA-seq data. The execution halted at LeafCutter differential splicing analys…
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### Is your feature request related to a problem?
Is there a way to do differential expression of transcripts (e.g. similar to DEseq2 but for transcripts) with RNAlysis?
### Describe the solution yo…
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### Description of feature
Differential splicing is a frequent consequence observed in RNA-Seq data. rMATS (https://rnaseq-mats.sourceforge.net/) is the most frequently used analysis tool, providing …
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This recent paper provides an overview of pipelines that can be used differential splicing analysis:
https://www.biorxiv.org/content/early/2017/06/30/156752
Figure 1 shows an overview of differ…
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Hi All,
I would like to know if we could use the paired samples ( same donor sample in two conditions ) for differential splicing analysis. How can I include the pairing information in group file ?
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Hi yang,
Here are two quick question: 1) if we want to merge multiple sample of AS single cell data, what strategy do you recommend to use to remove batch effect? 2) the RNA velocity analysis …
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Hi @EricKutschera , I am currently using rMATs-turbo to detect alternative splicing events between two conditions. From the recently published paper, "A large scale binding and functional map of human…
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### Error in differential_splicing(counts, numeric_x, confounders = confounders, : unused arguments (init = opt$init, seed = opt$seed). How to solve this problem?
- scripts: /leafcutter/scripts/l…
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### Error in differential_splicing(counts, numeric_x, confounders = confounders, : unused arguments (init = opt$init, seed = opt$seed). How to solve this problem?
- scripts: /leafcutter/scripts/l…
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Context: I have paired-end RNA-seq data from a stranded library preparation protocol. I would like to identify differential splicing events between two groups (including cryptic exons). Is it possible…