Aligning Paired-end file in R/Rstudio using align function


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!





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