Sorry if this may appear like a really dumb question, but I am new to RNAseq and feeling lost about some of the terminologies and calculations used in literature.
I understand what's the difference between the principle behind paired-end and single-end reads, however I need to clarify the method to calculate number of reads in paired end vs. single end reads.
For single end reads, I was told that I could calculate the no. of reads by: wc -l <name of="" fastq="" file="">, divided by 4.
For paired end reads, because 2 files are generated (R1, R2), so is it correct that I calculate the number of reads by adding the read count derived from R1 and R2?
Thank you very much for your clarification.