Question: Error while running HISAT2
gravatar for rob.costa1234
13 months ago by
United States
rob.costa1234150 wrote:

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.



rna-seq • 1.0k views
ADD COMMENTlink written 13 months ago by rob.costa1234150

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

ADD REPLYlink written 13 months ago by h.mon24k

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

ADD REPLYlink written 13 months ago by WouterDeCoster37k

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

ADD REPLYlink modified 13 months ago • written 13 months ago by genomax64k
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