I downloaded some fastq files from SRA for analysis. I aligned them to my genome of interest using STAR, but now I'm not sure if my process was correct. My goal is to get a count matrix and analyze the data in Seurat. I used STAR's quantMode to get a count matrix, but the output only has 3 columns, i.e. three cells. This is obviously not the desired outcome. Now I'm wondering if I needed to split the fastqs into individual files for each cell/sample, or if the cell information is retained in the alignment bam file and I can use featureCount or htseq or something else to create a correct count matrix. Edit: This is Fluidigm C1 data
What single-cell protocol does it use?
They used Fluidigm C1
Hm, I'm unfamiliar with the output of that protocol. You may want to find some papers that utilize it and see how they generate their counts.
You may need to use one of these scripts to do the analysis of Fluidigm data.
I think you're right. There is a "C1 mRNA Seq HT Demultiplex Script" available here https://www.fluidigm.com/software that I believe will do what I need
david.f.stein : Please edit your original post and add in bold letters that this is Fluidigm data. It will have to be reprocessed properly before you can start doing counts.