How to extract a specific gene sequence for a specific cell from scRNA-seq fastq file

Question

[cook.675]

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!

Answer 1

[mahmoud.s.fahmy]

A similar post, here.

You would have to first align the raw reads to the reference genome.

[cook.675]

Thanks for that link, one quick question:

All the reads we have are transcript reads, I could then map to the transcriptome instead of the genome?

Im going through this now, I created the SAM file from paired end fastq's following this tutorial: https://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial

And am now converting them to BAM, and I will have to search for the next step