file size of pair-end sequencing fastq

Question

[Pei]

Hello everyone!

Do you think I should expect R1 and R2 fastq files have similar, or even equal, size? I mean the length of file measured in bytes.

Thanks!

Answer 1

[liorglic]

Depends. If you are talking about Illumina data which did not undergo any processing, than you should expect R1 and R2 to have exactly the same size (in bytes). However, if the files are compressed (.gz/.bgz) or are the result of some preprocessing or cleanup step (Trimmomatic, Cutadapt), then you might see slightly different sizes. In any case, the difference should be minor. Another way to QA your files would be to count the number of lines (wc -l) - should be the same in R1 and R2 (make sure it is divisible by 4), or just run FastQC.

[Pei]

Hi liorglic! Thanks!

[Pei]

In my case, the two fastq, R1 and R2, have an identical size after gunzip. but the size of R1.fastq.gz is 1.26 fold of R2.fastq.gz.

Cheers!