HISAT2 error: fewer reads in file specified with -2 than in file specified with -1


Does anyone know why I might be getting this error?
I’m trying to use HISAT2 on forward and reverse reads of files.
I would think that it wouldn’t matter how many reads were in the forward vs. reverse files.

Dont know much about exceptions but in general you always need to have the same number of forward and reverse reads. You can double check the number of reads with fastqc. The main question is why are the number of reads not equal? Did you do any pre-steps like quality trimming? In that case make sure you use a tool that is designed for paired-end data.

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