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  • Does TopHat support Unix piping?

    Hi,

    I know Bowtie supports piping (although not so convenient to use for paired-end reads), and I am wondering if TopHat does the same. I tried something like "gzip -dc $fq | tophat $genome -" but it doesn't work. Did I do anything wrong? Or if there are other ways to run TopHat without decompressing the sequence files first? Please feel free to share your tips/suggestions. Thanks a lot!

    -- Leo
    Last edited by HTS; 10-05-2010, 08:08 AM.

  • #2
    I would also like to know... I tried some bash process substitution, nothing seems to be working.

    Comment


    • #3
      A trick for using pipes with programs that don't normally accept anything on standard input is to specify the input file as /proc/self/fd/0. So for tophat that would be:

      Code:
      gzip -dc foo.fastq.gz | tophat genome /proc/self/fd/0
      Of course you're out of luck if you have paired-end reads.

      Note that this is Linux-specific. It won't work on MacOS and I'm not sure about other Unixes.

      Comment


      • #4
        Hm, that's giving me the same error that the process substitution did. Let me know if it works for you. Is this a shell-specific thing?

        Comment


        • #5
          Ah, it looks like tophat needs to seek() in the fastq file which means streamed input won't work at all. Sorry, looks like this does need to be uncompressed to disk after all.

          Comment

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