Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #31
    Originally posted by Dario1984 View Post
    You need to have the path to the bowtie2 executable file in your PATH environment variable.
    I did it before but doesnt work even included bowtie2-build and bowtie2-inspect

    thanks

    Comment


    • #32
      Originally posted by Ajayi Oyeyemi View Post
      [2013-02-18 16:06:49] Checking for Bowtie index files
      Error: Could not find Bowtie 2 index files (genome.*.bt2)
      Your soft-linking command is wrong.

      Instead of

      Code:
      $ ln -s ./Bos_taurus/NCBI/Btau_4.6.1/Sequence/Bowtie2Index/genome.*.
      Use

      Code:
      $ ln -s ./Bos_taurus/NCBI/Btau_4.6.1/Sequence/Bowtie2Index/genome* .
      Remember that soft-linking does not check that the target file exists, so you must make sure to get the syntax right. It won't give you any error if you make a mistake and link to a non-existent file.

      Comment


      • #33
        Thanks Dario. Did I get the soft-linking of the genes.gtf file? and is there a space between genome* and .(full stop sign). Sorry I'm a newbie...

        Comment


        • #34
          Originally posted by jsimba View Post
          even included bowtie2-build and bowtie2-inspect
          You're not allowed to put filenames in the PATH variable. You put the path to the directory which contains those programs.

          Comment


          • #35
            The GTF file is fine. Yes, read the man page for ln. The target and the link parameters are separated by a space.

            Code:
            $ man ln

            Comment


            • #36
              Bowtie error on tophat

              Originally posted by Dario1984 View Post
              You're not allowed to put filenames in the PATH variable. You put the path to the directory which contains those programs.
              Dario,

              I think there is a problem with the version of tophat for OSX seems that doesnt recognise bowtie2, I used this command:

              rsb-33-073:tophat-2.0.7.OSX_x86_64 jaime$ ./tophat2 /Users/jaime/Desktop/bowtie2_indexes /Users/jaime/Desktop/RNAseq/inoculated_libraries

              [2013-02-20 09:37:27] Beginning TopHat run (v2.0.7)
              -----------------------------------------------
              [2013-02-20 09:37:27] Checking for Bowtie
              Bowtie 2 not found, checking for older version..
              Error: Bowtie not found on this system.

              I put the bowtie2 in the tophat directory and try to run from there but bowtie is not recognised by tophat

              thanks

              Comment


              • #37
                Originally posted by Dario1984 View Post
                The GTF file is fine. Yes, read the man page for ln. The target and the link parameters are separated by a space.

                Code:
                $ man ln
                Dario...You are awesome! Thanks, I've finally got it to work.

                Comment


                • #38
                  You can also just build them yourself:

                  gtf_to_fasta /home/chris/databases/refAnnotation.gtf /media/chris/human/Sequence/hg19.fa /home/chris/databases/refAnnotationout

                  bowtie2-build /home/chris/databases/refAnnotationout /home/chris/databases/refAnnotationbt

                  Comment


                  • #39
                    Here is an answer to billstevens (many questions got intertwined):
                    It seems that you've already launched the tophat command (unsuccessfully) before, which led to the creation of an annotation.gtf.gff file from the annotation.gtf file. If you remove this file, the command should run smoothly.
                    Best,
                    Julien

                    Comment

                    Latest Articles

                    Collapse

                    • seqadmin
                      Strategies for Sequencing Challenging Samples
                      by seqadmin


                      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                      03-22-2024, 06:39 AM
                    • seqadmin
                      Techniques and Challenges in Conservation Genomics
                      by seqadmin



                      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                      Avian Conservation
                      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                      03-08-2024, 10:41 AM

                    ad_right_rmr

                    Collapse

                    News

                    Collapse

                    Topics Statistics Last Post
                    Started by seqadmin, Yesterday, 06:37 PM
                    0 responses
                    8 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, Yesterday, 06:07 PM
                    0 responses
                    8 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 03-22-2024, 10:03 AM
                    0 responses
                    49 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 03-21-2024, 07:32 AM
                    0 responses
                    66 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X