Question: Error while running HISAT2
gravatar for rob.costa1234
19 months ago by
United States
rob.costa1234170 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 • 1.5k views
ADD COMMENTlink written 19 months ago by rob.costa1234170

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 19 months ago by h.mon27k

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

ADD REPLYlink written 19 months ago by WouterDeCoster40k

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 19 months ago • written 19 months ago by genomax71k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1999 users visited in the last hour