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Determine the requirements and potential options for the basis of the Pangenome Annotation RNA-seq pipeline.
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Hello, I am following the pipeline of finding alternative splicing analysis using QoRTs and JunctionSeq.
I am working on tomato rna-seq data
I have used HISAT2 for alignment and used "--minMAPQ 60".…
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Hello,
I was reviewing the script in your repository and I came across a line where null="null.bed" is assigned. I'm trying to understand the purpose of this file and whether it needs to be created…
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Hi, when using the [usecase_rna_velocity](https://github.com/dynverse/dyngen_manuscript/blob/8370bf5ce8a4c9e78967122202ccfee56fd516f1/analysis/usecase_rna_velocity/1_datasets.R#L19)
```
pwalk(design…
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* RNA-level predictions: free energy changes associated with nucleotide changes within a window (X bp before, X bp after) a nucleotide change; screen for RNAse targets within sequences (not sure if th…
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In `deseq_init.R`, this [line](https://github.com/cnio-bu/cluster_rnaseq/blob/1146c9fff739136dd34a2dd978a3a2a4e1fc444a/scripts/deseq2_init.R#L65) removes genes with less than 10 counts in all samples.…
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Dear Lamian team,
Thank you very much for creating this tool, it looks really promising and useful for my analysis. However, I am facing an error.
I am studying the gene expression over time from …
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Dear @christopher-vollmers ,
Hello. I have been trying to run the test-run of your script using the example script you have provided.
Unfortunately I am getting the error shown below, and I cannot…
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I realized that I will be working with a very large number of samples representing data from over 20 conditions. The paper mentions - "PsiCLASS is designed to leverage the gene information across samp…
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Hello @longmanz ,
Thank you for the mixscale package. I have been able to run the vignette example as well as my own data without issues. However, when I include the split.by argument in all the f…