Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cuffdiff single end reads

    hello,

    am running cuffdiff between two single end reads and even thought it runs fine am getting a message as follows:

    using default gaussian distribution due to insufficient paired-end reads in open ranges.it is recommended that correct parameters be provided(frag-len-mean and frag-len-std-dev)

    when they say fragment length ,do they mean average read length?

    thanks,
    joji

  • #2
    Hi madsaan,

    Do you fix the problem already?
    I'm facing the same error message as well
    need your advice....

    Comment


    • #3
      hello edge,

      I initially thought fragment length meant read length.Mine was 84 bp and I gave that as read length and i ended up without the warning message but my results were the same.When I later searched for it in seqanswers forum I found that frag-len-mean refers to the total sequence length (actual read + the adapter used during making the library). Also,if you use the version 0.9.3 you will not get the warning.
      Hope this helps

      Comment


      • #4
        hi madsaan,

        Thanks for reply.
        I'm using the latest version of Cufflink 1.0.1 and run the following command"
        Code:
        Cufflink/cufflinks-1.0.1.Linux_x86_64/cufflinks -p 4 -G Homo_sapiens.GRCh37.62.gtf --library-type fr-unstranded tophat_out/accepted_hits.bam 
        Cufflink/cufflinks-1.0.1.Linux_x86_64/cufflinks: /lib64/libz.so.1: no version information available (required by Cufflink/cufflinks-1.0.1.Linux_x86_64/cufflinks)
        Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
        [19:26:23] Loading reference annotation.
        [19:26:37] Inspecting reads and determining fragment length distribution.
        Processed 33455 loci.                        [*************************] 100%
        Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges.  It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
        Map Properties:
               Total Map Mass: 77344272.10
               Read Type: [B]0bp single-end[/B]
               Fragment Length Distribution: Truncated Gaussian (default)
                             Default Mean: 200
                          Default Std Dev: 80
        [19:32:30] Estimating transcript abundances.
        Processed 33455 loci.                        [*************************] 100%
        My input file is 2X50bp, paired-end read.
        I'm not sure why Cufflink will detect it as "0bp single-end".
        Do you have any idea regarding the above error message?
        If I'm using the "-g" option, the progress worked fine but the result is the same as the default Cufflink (without -g and Homo_sapiens.GRCh37.62.gtf in the command) running result
        Code:
        Cufflink/cufflinks-1.0.1.Linux_x86_64/cufflinks -p 4 -g Homo_sapiens.GRCh37.62.gtf --library-type fr-unstranded tophat_out/accepted_hits.bam
        I was thinking just to assemble back the annotate transcript in my sample.
        Thanks for any advice to improve the progress.

        Comment


        • #5
          Edge, I am having the same error message. My dataset is 32bp single end. But cuffdiff gave the following message:

          > Map Properties:
          > Total Map Mass: 8533100.77
          > Read Type: 0bp single-end
          > Fragment Length Distribution: Truncated Gaussian (default)
          > Default Mean: 200
          > Default Std Dev: 80

          I still got all those outputs. Did you figure out what the problem is? I would appreciate it very much if you or anyone else share your insights.

          Clariet

          Comment


          • #6
            Any resolution on this issue yet?
            I still see "Read Type: 0bp single-end" in my cufflinks1.1.0 output.

            Comment


            • #7
              me too

              Edit: apologies for hasty posting- it was cuffmerge that was producing this message, not cuffdiff, which in fact displays more more sensible output (not sure why cuffmerge displays this though...).

              I'm also experiencing this problem with 1.1.0. The relevant lines:

              Code:
              16:19:28] Inspecting reads and determining fragment length distribution.
              Processed 28835 loci.                       
               Map Properties:
              	Total Map Mass: 731211.00
              	Read Type: 0bp single-end
              	Fragment Length Distribution: Truncated Gaussian (default)
              	              Default Mean: 200
              	           Default Std Dev: 80
              I'm using Illumana GAII 78 bp paired end so it doesn't make a lot of sense. I'm trying to determine if it impacts on the result.
              Last edited by pinin4fjords; 10-13-2011, 09:34 AM. Reason: Extra info

              Comment


              • #8
                anybody got solution ?

                Comment

                Latest Articles

                Collapse

                • seqadmin
                  The Impact of AI in Genomic Medicine
                  by seqadmin



                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                  02-26-2024, 02:07 PM
                • seqadmin
                  Multiomics Techniques Advancing Disease Research
                  by seqadmin


                  New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

                  A major leap in the field has
                  ...
                  02-08-2024, 06:33 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, Yesterday, 06:12 AM
                0 responses
                17 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-23-2024, 04:11 PM
                0 responses
                67 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-21-2024, 08:52 AM
                0 responses
                73 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 02-20-2024, 08:57 AM
                0 responses
                62 views
                0 likes
                Last Post seqadmin  
                Working...
                X