Tony Zhou

The lastest pipeline actually does NOT use the sequence of the linker. It just use the `--pattern` to locate the barcode segments and check if the barcode segments match the...

It is normal. R1 reads are only used to extract barcode and UMI sequences. R2 reads were mapped to the genome and used for quantification.

Hi, using mamba instead of conda will fix this problem. ``` conda install mamba mamba create -n celescope -y --file conda_pkgs.txt ```

I am afraid that mamba is the only solution here. If you are worried that mamba will mess up your base conda environment or you cannot install mamba in the...

https://github.com/stanford-futuredata/ColBERT/issues/309#issuecomment-1958028653 Similar issue here. This might help.

https://github.com/singleron-RD/CeleScope/discussions/27#discussioncomment-7881874 You can also try to install pysam with conda(mamba).

It complained that the gene expression matrix directory was not found the in `./result_celescope_KM1_total/*count/` ``` FileNotFoundError: No file found for ['./result_celescope_KM1_total/*count/*filtered_feature_bc_matrix', './result_celescope_KM1_total/*count/*matrix_10X'] ``` Did the `celescope rna` pipeline complete successfully?

CeleScope does not have such function. You can simply normalize the data in downstream analysis. https://github.com/satijalab/seurat/issues/672

1. I have checked one run(SRR19312208) of GSE203360 and it is scopeV1. 2. `Exiting because of FATAL ERROR: could not create FIFO file` Please take a look at https://github.com/alexdobin/STAR/issues/1776 You...

Sorry. It needs to be double quoted, like this `--STAR_param "--outTmpDir some_dir"`