I have two fastq reads (R1 and R2) for single cell rna-seq data.
R1 is 9.5GB and R2 is 19.5 GB. As far as I know R1 is usually the barcode read and R2 is the cDNA read.
I am trying to follow the galaxy pipeline Pre-processing of 10X Single-Cell RNA Datasets
But in this training 4 files are used, two files for each reads. I only have two files, one file per read. I used R1 as barcode read and R2 as cDNA read as the input parameters for rna star solo. But I got an error in generating alignment bam file and all the other files were empty.
Can anyone help me figure out? I am new to this whole thing.