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Fastx Quality Filter

Wanted to if any one can help me run the fastq quality filter. Every time I run it I get and error messages fastq_quality_filter: input file (-) has unknown file format (not FASTA or FASTQ), first character = (10)

All I am doing changing directory into the FastX directory then dragging in the fastq_quality_filter followed by dropping in my fastq file I hit enter nothing happens and I hit enter what it gives me is the error message above. Can anyone help me, Is something I am doing wrong when inputing into terminal.

fastx fastq
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updated by moorem moorem • written by freddy • freddy

Character 10 in ASCII is a line-feed character. Unix, Mac, and Windows all use different systems for end-of-line characters. Maybe that's the problem? Or there is a blank line at that start of the FASTQ file?

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written by Torst Torst

edit your post and add both the command line that you execute as well as the results of:

head -5 yourfile.fq
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written by Istvan Albert Istvan Albert

1 answer

What is your full command? Is the -Q 34 (or alternative) missing, to indicate ASCI status?

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written by moorem moorem

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