This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Seeking assistance in scRNA Seq

Hi all,

I am currently learning scRNA-Seq analysis using Seurat, for which I downloaded the barcodes and features (and not the raw fastq files), and I am using the scripts that have been provided. In the set of files uploaded, the authors have not provided us with the *.h5 files to identify the doublets.

I was able to find a python script to generate the *.h5ad files from the barcodes and features, but when I run scanpy.read_10x_h5(), I get an error saying my file has more than one genome, and upon running it using any of the genome options (such as X, obs, varm), I get an error saying more files are needed.

My question now is, is it acceptable to generate the *.h5ad files from the barcodes and features, or is it to be done with the raw data? And if anyone is able to give me a solution to my above issue, it would be highly appreciated.

Thanks in advance

python scrna-seq r
• 1,120 views • link
written by vinayjrao vinayjrao

You need the counts as well, which are often in market matrix format. If you have all three of those files you can read them into scanpy directly with read_10x_mtx.

• 0 views • link
written by rpolicastro rpolicastro

Hi,

Thnks for your reply. I do have the matrix file too. I will try that and update

• 0 views • link
written by vinayjrao vinayjrao

0 answers

No answers yet.

Log in to answer this question.

More posts like this