Hello! I have paired-end data but when I initially converted it to Fastq (from SRA) I forgot to spit the file so I ended up with Fastq files with read length of 200 (due to both forward and rev strands being combined).
Now I've correctly redone the SRA-> Fastq conversion but I'm wondering if it is necessary? Can I just use the original file rather than the split one? For example, if I used only the forward strand for my analysis wouldn't I get less reads aligned than if I used the file with both strands combined? I don't know if this would cause issues in the function.
Here is my code: align(index="./path/full_hg19", readfile1 = "./path/Sample.fastq")
Any help would be appreciated!