I am trying to work on a public experimental scRNA-seq dataset of 12 samples. These samples are pooled with 10x Chromium. I have the SRA accession Ids and have already downloaded the BAM files in the Galaxy server. However, I am not sure how I can extract the count matrix from these samples using the Galaxy server. Usually I run Cell Ranger to extract the counts data, but apparently I do not have the computational resources available. Are there any pipeline/tool available to do this in Galaxy Web Server?
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Hi @mdka00001 Welcome to GalaxyHelp!
That is definitely a beneficial question for many. If you have SRA accessions, please download the FASTQ files instead of BAM files and follow the 10x preprocessing tutorial: Hands-on: Pre-processing of 10X Single-Cell RNA Datasets / Pre-processing of 10X Single-Cell RNA Datasets / Single Cell
You would have to map them again but STARSolo gives you count matrices that is ready to use with Scanpy or Seurat on Galaxy.
Here are more tutorials on that: Single Cell / Tutorial List
Please let us know how it goes or if you have further questions.
All the best,
Pavan
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