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Vivianstats / scImpute

Accurate and robust imputation of scRNA-seq data
https://www.nature.com/articles/s41467-018-03405-7
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About the 'genelen' #33

Open zh-Bian opened 3 years ago

zh-Bian commented 3 years ago

"'genelen' must be specified when type = 'TPM'!". Different version of genomic has different length? And the file in UCSC is about the whole length, not the cDNA. Could you tell me where can I download the suitable genelen for human and mouse? @Vivianstats

Vivianstats commented 3 years ago

Hi,

It would be best to calculate gene length based on the same reference version you used to align the reads. I'm not sure if there is such information readily available for download, but you can also calculate the length using the information in the GTF files.

Best, Vivian