Hello everyone,
I run STARsolo to obtain the filtered count matrix for scRNA-seq data. Currently, I am trying to perform clustering. My goal is to obtain a file (in csv, tsv, ...etc format) that has each cell barcode and its corresponding cluster/group name/number.
I have a very little background about clustering as a beginner and I am confused. Any guidance on walking me through this process to reach my goal would be highly appreciated.
Thank you so much in advance.
Cheers, Yousry
2 answers
I'd recommend doing some reading. You're getting ahead of yourself, you should learn to import your data into R/python, perform QC, normalize, etc, before attempting to cluster. I'd highly recommend you give OSCA a close read. It's easy to follow, provides good context, and has many code examples. Even if you use scanpy or Seurat instead, it'll help you recognize why certain steps are necessary.
The two most common ways to analyze single cell data are either with Seurat or with bioconductor. You can google for how to use Seurat, here's a link to the bioconductor guide:https://bioconductor.org/books/release/OSCA/
Log in to answer this question.
-
Forum: Recommendation and Advice
written by Sabina •
-
Forum: Advice for transitioning from a Life Sciences Education degree to Bioinformatics
written by mireader11 •
-
scRNA datasets integration
written by mrashad
-
Forum: Looking for Entry-Level Bioinformatics Project Ideas to Build My Portfolio
written by Samudraneel •
-
Identifying common DEGs among multiple datasets
written by Shma •
-
CDHIT para and cdhit slow speed
written by ahteshamabbasi1996 •
-
STARsolo detected only one gene and Features.tsv file is empty
written by MYousry •
-
Filtering reads from aligned scRNA reads BAM file by filtered cells barcodes (CB)
written by MYousry •
-
Should I normalize the data before or after filtering to a particular cell type?
written by gt •
-
scRNA-seq gene expressions from small number of cells
written by mvis1231
See the OSCA, Seurat, or Scanpy vignettes.