# How to extract count matrix from BAM files of scRNA-seq experiment in Galaxy Server?

**URL:** <https://help.galaxyproject.org/t/how-to-extract-count-matrix-from-bam-files-of-scrna-seq-experiment-in-galaxy-server/15207>\
**Category:** usegalaxy.org support\
**Tags:** single-cell, rna-seq, featurecounts\
**Created:** [April 10, 2025, 12:19pm UTC](https://help.galaxyproject.org/t/how-to-extract-count-matrix-from-bam-files-of-scrna-seq-experiment-in-galaxy-server/15207 "2025-04-10T12:19:02Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mdka00001](https://avatars.discourse-cdn.com/v4/letter/m/c77e96/32.png) [@mdka00001](https://help.galaxyproject.org/u/mdka00001)\
**Post date:** [April 10, 2025, 12:19pm UTC](https://help.galaxyproject.org/t/how-to-extract-count-matrix-from-bam-files-of-scrna-seq-experiment-in-galaxy-server/15207/1 "2025-04-10T12:19:02Z")

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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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**Author:** ![pavanvidem](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/pavanvidem/32/1687_2.png) [@pavanvidem](https://help.galaxyproject.org/u/pavanvidem)\
**Post date:** [April 10, 2025, 12:48pm UTC](https://help.galaxyproject.org/t/how-to-extract-count-matrix-from-bam-files-of-scrna-seq-experiment-in-galaxy-server/15207/2 "2025-04-10T12:48:50Z")

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> [@mdka00001](#):
>
> 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?

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](https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-preprocessing-tenx/tutorial.html)  
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](https://training.galaxyproject.org/training-material/topics/single-cell/)  
Please let us know how it goes or if you have further questions.  
All the best,  
Pavan