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Thanks, dpryan!
It worked!!!
I didn't add '-i' in front of the input file, so the program couldn't find a input file.
Am I understanding right?
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Oh, I actually missed the "input file (-)" part of the error. An input file of "-" typically means stdin, which is the default for that command. Also, there is no "-Q" parameter, so that's likely ignored. The command should be:
Code:fastx_quality_stats -i 4.1.fastq
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The file doesn't seem to have blank at the start.
Code:$ head 4.1.fastq @HWI-ST908R:191:D27LWACXX:7:1101:4446:2397 2:N:0:CGATGT NNNNNNCNTCTTCNNNTGNGNNNNGNNCNTNGGGGAGACCNNGNNAANNNNNTTANNNGNNNANTNCCNNNNNNNNNGNNCNCTNNNNNNNNNNNNNNNNN + ##################################################################################################### @HWI-ST908R:191:D27LWACXX:7:1101:4422:2401 2:N:0:CGATGT NNNNNNTNAGCTTNNNAANCCNNTANNCAACTCATCCGAGNNTNNTTNNNNNGGCNNNGNNNCNGTCCNNNNNNNNNTGNCNCGGNNNNTNNNNNNNNNNN + ##################################################################################################### @HWI-ST908R:191:D27LWACXX:7:1101:4557:2387 2:N:0:CGATGT NNNNNNANTNTCNNNNCGNANNNNCNNNNCNNGNCGCTNCNNNNNNNNNNNNNTANNNNNNNGNNNTNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNN
Could that cause the problem?
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The error means that the first line of the file is blank. If that's true, then the file is screwed up. What does
Code:head 4.1.fastq
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fastx_quality_stats error : input file (-) has unknown file format
Hi.
I was trying to check qualities of my fastq files from RNA-seq using fastx-toolkit, but I kept getting a following error.
Code:$ fastx_quality_stats -Q 33 4.1.fastq fastx_quality_stats error : input file (-) has unknown file format (not FASTA or FASTQ), first character = (10)
Has anyone expreinced this?
Thanks!
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