Question: fastq_quality_filter: input file (-) has unknown file format (not FASTA or FASTQ)
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gravatar for 4galaxy77
4.1 years ago by
4galaxy7760
United Kingdom
4galaxy7760 wrote:

hi, so i'm running my RNAseq data through the Fastqc quality filter program through command line in Linux Ubuntu. 

I've used this input and this error comes up

user@it053392:~$ fastx_trimmer

[-q 30] [-z] [-i /home/user/Desktop/_sam/RNAseq Beta Data/10G87.fastq] [-o /home/user/Desktop/RNA]
fastx_trimmer: input file (-) has unknown file format (not FASTA or FASTQ), first character = [ (91)

Any ideas what the problem is. The file is tagged as being .fastq format and I've just used the same files in another Fastx programme (which visualises the data quality), so I'm a bit confused as why it won't work. Any help?

 

 

 

rna-seq software error • 1.8k views
ADD COMMENTlink written 4.1 years ago by 4galaxy7760

Have you looked at the actual file contents, for example by using the head command?

ADD REPLYlink written 4.1 years ago by Joseph Pearson450
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