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ShouWenWang-Lab / snakemake_DARLIN

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Is it necessary to substitute the "10xV3_barcodes.txt.gz" with a custom barcode list? #6

Open Selecton98 opened 5 months ago

Selecton98 commented 5 months ago

Hi Shouwen,

I'm using the snakemake MATLAB CARLIN pipeline, cfg_type : 'sc10xV3' , template : 'cCARLIN'.

Is it necessary to substitute "10xV3_barcodes.txt.gz" with a custom barcode list, such as the one generated from the matched Seurat object? If not, does the "10xV3_barcodes.txt.gz" include all the possible barcodes if I follow the same protocol?

Thank you, Sunny

ShouWenWang commented 5 months ago

If you use the 10X V3 method, then the 10xV3_barcodes.txt.gz file should include all the valid cell barcodes. You do not need to include your own.

Alternatively, you may try our python pipeline:

snakemake -s $code_directory/packages/snakemake_DARLIN/snakefiles/snakefile_python_DARLIN.py  --configfile config.yaml --core 10

It will use notebook under 

QC/single_cell_DARLIN-10x.ipynb

We have made key changes over time. If you run into problems, please 'git pull' to update the latest changes from github.

Selecton98 commented 5 months ago

Thank you. That makes sense.