Question: Pseudotime on scRNAseq TPMs?
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gravatar for m.fletcher
12 weeks ago by
m.fletcher20
Germany
m.fletcher20 wrote:

Hello all,

I was trying to figure out if I could re-analyse the data from this single-cell RNAseq paper: http://science.sciencemag.org/content/344/6190/1396

Ideally, what I would like to do is calculate some pseudotime trajectories using the deposited expression matrix (ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE57nnn/GSE57872/matrix/GSE57872_series_matrix.txt.gz)... but of course I've just realised that most pseudotime methods work from the raw counts, which is (I believe) not available for this dataset.

(And no, you can't recalculate the counts from the TPMs, because the matrix deposited has been filtered in slightly weird ways)

Does anyone know of a pseudotime method that would work with TPMs? Or do I have to find some other way of doing this analysis?

Cheers in advance!

scrnaseq pseudotime tpm • 120 views
ADD COMMENTlink written 12 weeks ago by m.fletcher20

This page listed all pseudotime analysis algorithms. Worth exploring to check if any of these can do the job you want?

ADD REPLYlink written 9 weeks ago by venu6.1k
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