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Swarbricklab-code / BrCa_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
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Gene Positions data for running inferCNV. #29

Open purvapruthi opened 1 year ago

purvapruthi commented 1 year ago

Hello,

Thank you so much for providing this data. I am new to the field of single-cell analysis. So, this might be a naive question. I was looking to reproduce the inferCNV pipeline and was wondering where can I get the gene positions file: infercnv_gene_order.txt.

Thanks.

johnyaku commented 1 year ago

Hi @purvapruthi.

I've added infercnv_gene_order.txt to inferCNV/refs.

You'll need to adapt the ref_dir variable to your own system in order to get the code to run.