fastq_quality_filter: input file (-) has unknown file format (not FASTA or FASTQ)
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8.8 years ago
4galaxy77 2.8k

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 • 3.3k views
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Have you looked at the actual file contents, for example by using the head command?

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