Aligned BAM file to gene-cell expression matrix for scRNA-seq
0
2
Entering edit mode
19 months ago
awells2 ▴ 20

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 • 1.4k views
ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1648 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6