I have a scRNA seq experiment where I would like to look at the raw sequencing data for one specific gene.
We have 3' ends, and the sequence may or may not be different depending on the cell type we are looking at.
I have the list (barcodes) from the cells we are interested in looking at, to see what the sequence is, and if its different for the different cell types.
How would I find and extract this information from the fastq files? We have paired end sequencing
Thanks in advance!