Different reads number in the ENCODE paired-end RNA-seq data

Question

[biock]

Hello, I'm analyzing some RNA-seq data from ENCODE. I found some fastq files from the same run may have different number of reads (e.g. ENCSR245ATJ and ENCFF215BFI), which will cause an error when I run hisat. How to deal with this issue? Thank you!

[seidel]

some fastq files from the same run may have different number of reads

What do you mean exactly? In many contexts a "run" can give rise to many fastq files with nothing to determine that the number of reads should be equal between them. Can you be more clear? What sort of problem are you having with hisat?