Question: Any alternatives to Cellranger aligner that Seurat can read?
0
gravatar for louis-gil
4 weeks ago by
louis-gil0
louis-gil0 wrote:

Are there good alternatives to Cellranger aligner that Seurat can read? Or any methods of converting default output from Star to the Seurat readable format?

ADD COMMENTlink modified 4 weeks ago by ATpoint42k • written 4 weeks ago by louis-gil0
2

Seurat just takes a count matrix with cells as columns and features as rownames. There are a ton of programs now for processing single-cell data, so any specific advice would need more information about your project structure.

ADD REPLYlink written 4 weeks ago by rpolicastro2.3k

The output of cellranger is compressed in 3 files (barcodes, features, matrix) which contain a compression of the count matrix and HTO info. Seurat, decompressed into a count matrix. I'm basically asking if there are any programs that use the same output as cellranger.

ADD REPLYlink written 4 weeks ago by louis-gil0

Seurat has a function (Read10X) to make it easier to read Cell Ranger output. It converts that output to a matrix. You don't have to use that function. CreateSeuratObject() requires a standard R matrix.

ADD REPLYlink written 4 weeks ago by igor11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2124 users visited in the last hour