Number of reads in paired end fastq files

[bong28]

I have two fastq files from paired end sequencing. I got those two files after converting a bam file to fastq. I was doing a quality check on the files, when I saw the number of sequences option in FASTQC tool gave different number for both files.
The number of sequences for read 1 was : 508168252
The number of sequences for read 2 was : 512336921

Shouldn't this be the same?

[GenoMax]

Normally yes.

I suggest that you use use "repair.sh" from BBMap suite to re-pair the reads and remove singletons to a separate file. Assuming your conversion has properly worked.

[bong28]

Thanks for your reply