I don't understand the HDF5 file from 10x genomics scRNAseq

Question

[jonas.andersson]

Hi!

I have recently started my Phd and I'm trying to open a hdf5 file in R. The file is generated from 10x genomics cell ranger pipeline.

Can someone please explain what i, P, Dim, Dimnames,x and factors means or link to someplace i can read more about it in detail. I have tried google but haven't found anything good:/

Dimnames[1] and Dimnames[[2]] are obviously the identified genes and the barcodes. But i don't understand what the others are.

please help me!:)

best / Jonas

[ahmad mousavi]

you should read the Seurat manual, may find the answer of the Items you mentioned.

[jonas.andersson]

thx for the tips! you are right, I need to start from the basics:)

Answer 1

[ATpoint]

It's a compressed matrix format that you are looking at, rows are genes, samples are columns, but there is not much to "see" there for the human eye other than a lotm of integers and mainly zeros. In any case, by eye you are not going to run any analysis. As suggested already you should follow a guided tutorial such as Seurat or my favourit the extensive Bioconductor single-cell book https://bioconductor.org/books/release/OSCA/ to get started. Basically, you need to transform this into an analysis object, in Bioconductor that would be the SingleCellExperiment format, and then get analysis going, as e.g. described in that book. Does that make sense to you?

[jonas.andersson]

thx, I will check this out!