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I recently attended HCA Asia, and an attendee requested that Ensembl transcript IDs would be accepted as feature variables for the count matrix, especially for Smart-Seq data. He noted that the reason…
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Hi Kristoffer,
I understand that each cluster generated by isONclust represents all reads that came from the same gene.
However, I was looking for a de novo tool/method that could determine wh…
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Hello, your software is doing a great job and I am very grateful for developing such a good tool. I am currently using this tool for alternative splicing analysis. I have a question about the results …
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Hi,
I am currently working on RNA seq data (Paired end), of human sample, I need to check the alternative splicing event of a specific gene "NEK1" in the sample data, and may be after that for all th…
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Hi,
I aimed to detect novel transcript with HIFI reads using stringtie2(guided mode). Then I compare the result to gencode(v44) annotation. But almost half of the novel transcripts are marked as "s".…
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> [!NOTE]
> This proposal is scoped to more or less `mkDerivation`, so individual packages, and it does not affect package _sets_ in any significant way.
### Describe the problem
This issue pro…
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Hello,
I am currently using rMATS to identify alternative splicing events between several samples (.bam) for two conditions, but I need to perform batch correction and normalization of the junction…
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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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### Description
I installed `outrigger` using the `environment.yml` file and didn't get the command line entry points, so I installed via `pip` and then got errors with the C libraries of `pysam`.
…