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  • guzip paired fast.gz files

    Hello,
    I have a bunch of paired fastq.gz files, and I need to decompress them for further low quality data trimming.
    However gunzip command is not working on paired files. Any suggestions?

    this is the error output
    gzip: file.fastq.gz: unexpected end of file

    Thank you!
    Last edited by Kaskere; 09-01-2020, 01:36 AM.

  • #2
    Are you sure the files are gzipped (is spite of what the extension says)? What does

    Code:
     file one_file.fastq.gz
    say?

    Comment


    • #3
      Originally posted by GenoMax View Post
      Are you sure the files are gzipped (is spite of what the extension says)? What does

      Code:
       file one_file.fastq.gz
      say?
      myfile.fastq.gz: gzip compressed data, from FAT filesystem (MS-DOS, OS/2, NT)

      they are compressed..

      These paired end files were obtained after PE Trimmomatics

      Comment


      • #4
        Try using "zcat" to see if it can display the file contents like:

        zcat file.fastq.gz

        If it displays the file contents, then redirect the output to a new file like:

        zcat file.fastq.gz > new_file.fastq

        Comment


        • #5
          @kaskere: Were these files compressed using Windows zip program? You may need to use "-S .zip" option for gunzip.

          Comment

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