Question: Error while running HISAT2
0
gravatar for rob.costa1234
13 months ago by
rob.costa1234150
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.

Thanks

Rob

rna-seq • 1.0k views
ADD COMMENTlink written 13 months ago by rob.costa1234150
2

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
2

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
1

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.

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