Comments (3)
Hi Wendell,
Sorry for the inconvenience, celescope's documentation really needs to be improved.
Assume that you need to use the rna
pipeline.
In celescope V1 version we need to combine each tools so here is a slightly more detailed step-by-step explanation.
https://github.com/singleron-RD/CeleScope/blob/v1.15.0/docs/rna/multi_rna.md
In celescope V2 version, we use STARSolo and STARsolo does all the heavy lifting (demultiplexing and error correction of barcodes and UMI, mapping, quantification), so the entire rna
pipeline is basically a wrapper of STARsolo.
After STARsolo generates the expression matrix, scanpy is used for clustering and dimensionality reduction. The specific code is here
https://github.com/singleron-RD/CeleScope/blob/master/celescope/tools/analysis_wrapper.py
Additionally, we are rewriting all pipelines in Nextflow. Hopefully this will make the workflow more transparent to users and produce better documentation.
Sorry again for the inconvenience. If you have more questions about installing and running celescope, I'd be happy to answer them.
from celescope.
Hi Wendell, I just created a repo for analyzing singleron RNA data based on nf-core scrnaseq best practice, hope you find this useful.
https://github.com/zhouyiqi91/scrnaseq
from celescope.
Hi @zhouyiqi91,
Thanks for the additional links and information. I managed to start my runs and am waiting in the outputs, but will look into the nf-core pipeline for the analysis of my next datasets.
Best Regards,
Wendell
from celescope.
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