How to get Gene level TPM single cell Smart-seq2 data

Question

[luckysardar171]

Hello I am new to RNA seq and ScRNA-seq i have smart-seq2 data want to convert to gene level TPM for this I need gene length info how to get this information I tried to get the complete length of gene by substracting gene START and END but. I was going through many biostar threads gene length for calculating TPM values. Suggesting can't use the complete gene length for the gene level TPM any one please help me how to calculate gene level TPM from the GTF file.

Thank you

[Soheil]

May I ask why you need TPM normalization? In single-cell analysis, you don't need the TPM data for differential expression analysis or for plotting the expression levels.

[luckysardar171]

Soheil wanted to compare the gene expression within a sample so many suggestions were there TPM were the good options. any suggestion if not TPM what will be the better option for the expression levels in sc_RNA seq I wanted plot the heatmap

[Soheil]

I would only suggest TPM if you want to do a single-sample enrichment analysis. At the moment, that's the only case that I can think of for comparing gene expression within a sample. Otherwise, for the heatmaps - where you are typically interested in looking at the expression level of a gene across subpopulations/samples - you should be good with just the default normalization and scaling in Seurat. I suggest taking a look at the DoHeatmap function in Seurat. Seurat's team has done a great job documenting the tool. You can find the basic tutorial here https://satijalab.org/seurat/articles/pbmc3k_tutorial.html