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  • Install ea-utils

    Hi, I am new to Bioinformatics and Linux, I have dowloaded ea-utils 1.1.2-537 in my Ubuntu box and unzipped it. I tried to use the fastq-join with my paired reads but the following message appeared:
    fastq-joint command not found
    Is there something else i need to do to install ea-utils in my box?
    Thank you

  • #2
    I don't recommend fastq-join; in my tests, it's worse than pretty much every alternative other than Pear.

    Comment


    • #3
      Originally posted by sylvie.le.borgne View Post
      Hi, I am new to Bioinformatics and Linux, I have dowloaded ea-utils 1.1.2-537 in my Ubuntu box and unzipped it. I tried to use the fastq-join with my paired reads but the following message appeared:
      fastq-joint command not found
      Is there something else i need to do to install ea-utils in my box?
      Thank you
      Probably not (assuming ea-utils are already compiled). You may need to add execute permissions

      Code:
      $ chmod u+x /path_to/fastq-join
      or provide full path to fastq-join as you try to run it

      Code:
      $ /path_to/fastq-join your_R1_file your_R2_file

      Comment


      • #4
        Thank you, I tried but it did not work. In the ea-utils folder I have fastq-join.c, I dont know what is the meaning of the letter c....

        Comment


        • #5
          Originally posted by sylvie.le.borgne View Post
          Thank you, I tried but it did not work. In the ea-utils folder I have fastq-join.c, I dont know what is the meaning of the letter c....
          That means it is source code that needs to be compiled. There should be a readme-type document included in the source to tell you how to compile the code to make executable files.

          Generally a
          Code:
          $ make
          in the directory may be all that is needed.

          Comment


          • #6
            you mean this:

            make home/sylvie/desktop/ea-utils.1.1.2-537/

            or make home/sylvie/desktop/ea-utils.1.1.2-537 ?

            Comment


            • #7
              Code:
              $ cd /home/sylvie/desktop/ea-utils.1.1.2-537
              $ make
              Good guide for basics of unix for a biologist: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

              Comment


              • #8
                fastq-join works OK, you just need to relax it because it is so stringent. I use -m 30 -p 30 with good success. Some data is crappier than other data and may need additional grooming before it can be successfully merged.

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                • #9
                  Late here:
                  Last I recall installing, ea-utils needed libgsl-dev library to install
                  Bioinformaticscally calm

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