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  • Linux Command for joining left & right hand reads

    I know that there's a tool in Galaxy called 'Fastq Joiner' in which 2 fastq files (one with left & one with right hand reads) are joined together.
    Is there a simple Linux command to do the same thing? Something with the 'grep' command perhaps?

  • #2
    I don't quite understand. Would the "cat" or "paste" command be sufficient?

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    • #3
      Apologies, instead of 'grep' I meant 'paste'. Like you said I tried paste file1.fastq file2.fastq

      But I'm not sure that this command does the same as the 'fastq joiner' tool in Galaxy

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      • #4
        You'd need a small perl script to read in the sequence identifiers to imitate the galaxy joiner. I don't think there's a simple linux command unless your files are both in the same order.

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