I have a transcriptome data of 10.8gb R1.fastq and R2.fastq each. I then compressed these pairs using `gzip R1.fastq` and `gzip R2.fast2`, and now the files are 2.2gb and 2.4gb. Is it possible for two compressed files to have different size when the uncompressed files are of same size?
A wild guess... Second-in-pair reads usually have base qualities that drops faster along the read compared to first-in-pair. This makes the quality line on each fastq record more variable (i.e. more random and less compressible) in R2 than in R1.