Question: Aligned BAM file to gene-cell expression matrix for scRNA-seq
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gravatar for awells2
9 weeks ago by
awells20
awells20 wrote:

Hello everyone,

I am new to single cell RNA sequencing analysis and have been stuck on how to convert from .bam files to a gene-cell expression matrix. I am currently looking at data from the site: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR10349606. I have downloaded the .bam file, and have been following the tutorial https://scrnaseq-course.cog.sanger.ac.uk/website/construction-of-expression-matrix.html. The tutorial talks about how to go from a fastq file to the gene-cell expression matrix, however it is my understanding that the .bam file I downloaded has already been aligned to a genome. I also looked into using featureCounts (bioconductor), but this required a cellbarcodeList, which I am unsure how to obtain.

Can someone point me in the right direction? I think I have a conceptual misunderstanding about this process.

Thank you!

rna-seq R • 168 views
ADD COMMENTlink written 9 weeks ago by awells20

You can use featurecounts directly on the BAM file which is what the tutorial is doing. Then you can use umi-tools to count the output to generate the gene-cell expression matrix -if your data has UMIs-.

ADD REPLYlink written 9 weeks ago by emre.cto0
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