Closed francescabasini closed 10 months ago
Hi,
Can you explain a little more what you are looking for? I think the gene expression files here are already total-counts normalized.
Thanks a lot for your reply! Essentially, once I download the "stateFate_inVitro_normed_counts" and opened it, I can see a txt file with 3 columns and I am just trying to make sense of them.
Is it correct to assume that the first column indicates a gene, the second the cell it belongs to and the third is indeed the normalized count for that gene expression?
If that is the case, how can I associate each cell to the timepoint it's been profiled at? is it correct to assume that file "stateFate_inVitro_metadata.txt.gz" which has 130888 rows summarises all info for the normalised counts data?
Many thanks again
Hi,
Yes that's right! (except first column is cells and second column is genes)
Hi, there are 25289 columns in the "stateFate_inVitro_normed_counts.mtx.gz" but only 25288 genes in the stateFate_inVitro_gene_names.txt.gz, is it correct?
And it seems that "stateFate_inVitro_gene_names.txt.gz", "stateFate_inVivo_gene_names.txt.gz" and "stateFate_cytokinePerturbation_gene_names.txt.gz" are the same files, is it correct?
There are 25289 gene names in stateFate_inVitro_gene_names.txt.gz. Sometimes gene lists end with a newline character whereas this one doesnt, so make sure you read the final line.
And yes it's correct that all the datasets share the same set of gene names.
Apologies if this might seem a silly question but I have been having trouble trying to find normalised gene expressions for each single cell for genes annotated as variable for the in vitro dataset. Could you please indicate me a way to download them?
Many thanks