Entering edit mode
6.1 years ago
rob.costa1234
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310
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
How did you trim the fastq files? Did you trim each file of the pair separately? Because if you did, you shouldn't.
The error means that you don't have the same number of reads in the forward as in the reverse file.
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.