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  • Post a few lines from clc_trim_pair4.fq. Are you getting that error right away?

    Code:
    $ head -6 clc_trim_pair4.fq

    Comment


    • Originally posted by GenoMax View Post
      Post a few lines from clc_trim_pair4.fq. Are you getting that error right away?

      Code:
      $ head -6 clc_trim_pair4.fq
      This is what I get:
      @No_name
      CAACATTACCTAGTGCAAGACAGTGTTAATTTGAAGGCAGTTCATA
      +
      IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
      @No_name
      TTTTTTTTTTTTTTTTCTTTTCTCAACTTCCTTCACCTTCACACTCTCTTTCCCTTCTTC

      Comment


      • Is that all the sequence in the file? Just one record?

        If not, are all sequences called "NO_name"? That is not going to work since the names are not unique.

        Post output of.

        Code:
        $ ls -lh clc_trim_pair4.fq

        Comment


        • Hi all,
          I've been trying to download Bowtie2.2.5 for Mac and followed instructions on this forum. The consistent error message I've been getting is: (ERR): Expected bowtie2 to be in same directory with bowtie2-align: /Applications/bowtie2-2.2.5/
          I've followed suggestions from others with this problem to address this and I've realized that bowtie2-align is not in the folder I am downloading. Is this normal? Do I need to retrieve it elsewhere? I assume I am missing something basic since I am new to all this. Thanks in advance for any help.

          Comment


          • bowtie2 web site appears to be experiencing issues at the moment (can't get to the 2.2.6 code). Are you downloading the pre-compiled binary zip file for OS X from this link: http://sourceforge.net/projects/bowt...owtie2/2.2.5/? After uncompressing the archive all files you need should be in the uncompressed folder.

            Comment


            • Thanks for the reply. Yes I've downloaded that file but it does not contain bowtie2-align.

              Comment


              • I just checked the zip archive and the executables are all there (there are multiple align versions, bowtie2-align-l,bowtie2-align-s etc). You should run bowtie2 like so

                Code:
                $ bowtie2 -help

                Comment


                • Got it, thank you!

                  Comment


                  • error message: bowtie2 installation on mac

                    Hello, I'm not familiar to informatics and I try to install Bowtie2 on mac. I download bowtie2 source file.zip
                    I unzip it then when I did 'make' I have this error message:

                    1 error generated.
                    In file included from aligner_swsse_ee_u8.cpp:56:
                    In file included from ./aligner_sw.h:73:
                    ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found
                    #include "simde/x86/sse2.h"

                    Could you help me.

                    Thank you

                    Comment


                    • Download pre-compiled binary for macOS from here.

                      Consider using "conda" to install these programs that will save you a lot of time/headache.

                      Comment

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