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Should the sequencing depth of different datasets and batch effect issues be considered when merging RNA-seq data from different cohorts for input?
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Hello,
I have a few suggestions that you might consider/ reject for future development of leafcutter and leafviz applications relating to support for export of results from both leafcutter and leaf…
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Hi, [Kallisto/BUSTools was recommended by Seurat](https://github.com/satijalab/seurat/issues/2813#event-3222404304) to perform RNA isoform/alternative splicing analysis. However, I didn't find the re…
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### Enzyme, ADAR (proof-read and correct mistakes in RNA)
[**ADAR editing enzymes** are found in all multicellular animals and are conserved in sequence and protein organization. The number of ADAR g…
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I am interested to perform the differential gene expression (DE) and alternative splicing analysis of my RNA-seq dataset using Texudo2 approach as recommended in Pertea et al., 2016 (doi:10.1038/nprot…
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Dear author,
As the title, is there any function in CIRI-long to catch isoforms' counts ?
Or how could I get isoforms' counts instead of circRNA-genes' counts ?
Thanks a lot.
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Hi,
Thank you for developing this useful tool. I successfully ran the main pipeline from the DropSeq vignette with my data and mostly observed the expected results.
However, I noticed that the P…
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Hi,
I have a question regarding the library size of scRNAseq simulation.
In total there are 2 simulations, one with a librarysize of 20 Mio and one with a librarysize of 5 Mio.
Is librarysize …
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Hi,
I am trying to run rmats in the HPC. I installed rmats in a new rmats environment in conda.
I activated conda and the environment, but somehow I just can't run it. I got several errors.
I f…