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  • Bowtie2 cannot read gzip format files

    Hey, everyone!

    The help document of bowtie2 have said that the files of reads could be gzip'ed.

    When I use the paired reads and try the argument ( -1 <m1> -2 <m2>), the bowtie2 can read the gzip'ed files.

    However, if I use the gzip'ed unpaired reads and apply the argument (-U <r>), the bowtie2 suggest that "Error: reads file does not look like a FASTQ file". The gzip'ed file can not be recognized.

    Does anyone have come up with this problem?

    Thank You!

  • #2
    # HOW to add GUNZIP support to ANY program that doesn't have it:

    mkfifo file1.fifo
    mkfifo file2.fifo
    gunzip file1.gz > file.fifo &
    gunzip file2.gz > file.fifo &
    bowtie -1 file1.fifo -2 file2.fifo

    Comment


    • #3
      Originally posted by earonesty View Post
      # HOW to add GUNZIP support to ANY program that doesn't have it:

      mkfifo file1.fifo
      mkfifo file2.fifo
      gunzip file1.gz > file.fifo &
      gunzip file2.gz > file.fifo &
      bowtie -1 file1.fifo -2 file2.fifo
      Thank You Very Much!

      This is very useful!

      Comment


      • #4
        Originally posted by earonesty View Post
        # HOW to add GUNZIP support to ANY program that doesn't have it:

        mkfifo file1.fifo
        mkfifo file2.fifo
        gunzip file1.gz > file.fifo &
        gunzip file2.gz > file.fifo &
        bowtie -1 file1.fifo -2 file2.fifo
        In many cases this will work, but not all cases. This doesn't work for programs that attempt to seek through files (low-memory fastq randomisation being one example that I've recently seen).

        Comment


        • #5
          I needed to add a "-c" to that command, otherwise gunzip will delete the original compressed file, i.e.
          Code:
          mkfifo file1.fifo
          mkfifo file2.fifo
          gunzip -c file1.gz > file1.fifo &
          gunzip -c file2.gz > file2.fifo &

          Comment


          • #6
            Originally posted by dsenalik View Post
            I needed to add a "-c" to that command, otherwise gunzip will delete the original compressed file, i.e.
            Code:
            mkfifo file1.fifo
            mkfifo file2.fifo
            gunzip -c file1.gz > file1.fifo &
            gunzip -c file2.gz > file2.fifo &


            this patch fixes fifo support, and also adds built-in gzip support to bowtie 1.0 (which remains the fastest, fastq->sam program out there)

            An ultrafast memory-efficient short read aligner. Contribute to earonesty/bowtie development by creating an account on GitHub.

            Comment


            • #7
              FYI, zcat is often a shortcut to 'gunzip -c'

              Also under BASH you should be able do something like:

              bowtie -1 <( zcat file1.gz ) -2 <( zcat file2.gz )

              or in the original posters question

              bowtie2 -U <( zcat file.gz )

              Comment


              • #8
                actually there's a bug in bowtie ... a race condition that can make it unreliable. you should not use fifo's unless you used the patched version that supports them

                An ultrafast memory-efficient short read aligner. Contribute to earonesty/bowtie development by creating an account on GitHub.

                Comment

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