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  • GenoMax
    replied
    That is correct. Some programs require an explicit "-i" to signify input.

    Leave a comment:


  • mbk0asis
    replied
    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?

    Leave a comment:


  • dpryan
    replied
    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

    Leave a comment:


  • mbk0asis
    replied
    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
    As I mentioned earlier, I used 'cat' command to merge four files.
    Could that cause the problem?

    Leave a comment:


  • dpryan
    replied
    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
    show?

    Leave a comment:


  • 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)
    RNA-seq was performed in Hiseq2000 (paired-end), and the guy who ran the sequencing gave me these files when I asked the raw sequencing data. I merged all the fastq files in each sample into one file using 'cat' command since I wated to map them as singe-ends.

    Has anyone expreinced this?

    Thanks!

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