Integration and Normalize with Smartseq2 matrix by gene length (human)

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1

Hi,
I’m using the Atlas-level integration and label transfer tutorial to integrate smartseq, 10x and InDrop. My data is from human and you recommend normalize the smartseq data by gene length, but the file to do the analysis is from mouse. Is there any file with human database?

Thanks in advance

2

Hi Gabriela,

If you have the gtf file, you can use gtf tools for getting the gene length. You can download gtftools from here.
Once you unzip the GTFtools_0.8.0.zip, you can run
./gtftools.py -l genelen.txt input.gtf
to get the genelength file.

3

Hi chenlingantelope

I would like to continue on this question. As Gabriela said, I want to run on human data. You mentioned to get GTFtools_0.8.0.zip. Does it mean that file is for human gene length to be used for SCVI label transfer?
Thank
W