How to import data from cell ranger to R (Seurat)? I will have some scRNA-seq data. The goal of the experiment will be to see if there is any difference in gene expression between treatment groups using the package Seurat from R.
I have read a tutorial how to do the analyze, but this tutorial does not explain how to import data.
I am a total beginner with R, I searched the internet,but the majority of the explanations related to csv/excel/txt... common files.
Data are from Cell ranger and spread in 3 files with following file extensions : .tsv and .mtx (barcodes.tsv, genes.tsv and matrix.mtx).
Collaborators ran Cell Ranger and gave these cell ranger output files : barcodes.tsv, genes.tsv and matrix.mtx.
Can someone give me the code to import these kind of data to R ?
Thank you in advance.
update: By &quot;directory&quot; you means &quot;folder&quot; on my computer for example ? So I need to save the 3 files under one folder and then to put name of the folder into brackets after the Read10x function ? I am a total beginner with R (I have used to R commander for statistical tests but that's it...).
update 2: I successed to import data into Seurat with the explanation of StupidWolf. I do not know C language ( I do not know almost any language ..). My system crashed a little further in the analyze after importing, not enough RAM... so now I am learning Linux commands to switch on the cluster.
Have a look here and the entire tutorial:
https://github.com/hbctraining/scRNA-seq/blob/master/lessons/03_SC_quality_control-setup.md