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Error while running HISAT2

I have paired end RNAseq data that has been trimmed individual AFSTq file, when I ran hisat2 it gives me following error-

Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

Any one can advice what may be wrong I tried to google it but no hit came.

Thanks

Rob

rna-seq
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written by rob.costa1234 rob.costa1234

How did you trim the fastq files? Did you trim each file of the pair separately? Because if you did, you shouldn't.

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written by h.mon h.mon

The error means that you don't have the same number of reads in the forward as in the reverse file.

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written by WouterDeCoster WouterDeCoster

You could repair.sh the data using BBMap suite or as @h.mon indicated, ideally go back and re-do the trimming with R1/R2 together.

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written by GenoMax GenoMax

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