Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Help: cufflinks stopped in one loci

    I used cufflinks to estimate gene expression in a gtf file, however, one sample could not pass one loci, always stopped there (all the other samples are fine); the command i used is as following:
    cufflinks -G XXX.gtf YYY.bam
    the error information is as following:
    You are using Cufflinks v1.1.0, which is the most recent release.
    [18:37:04] Loading reference annotation.
    [18:37:04] Inspecting reads and determining fragment length distribution.
    > Processing Locus chr21:9825743-9826389 [************* ] 52%

    this lasts for ever and I then changed --max-bundle-frags to 2000000, but still stoppped here; after that I went to gtf file to find the loci and deleted this loci, now it stopped in another loci, what should I do? delete another loci? helps please!!!

  • #2
    Then I tried:
    cufflinks YYY.bam
    (I plan to try cuffcompare YYY.gtf XXX.gtf later)

    it stopped in another loci...anything wrong with my .bam??? please help...

    Comment


    • #3
      all stopped, because bam is too big so cufflinks crashed? please help, thanks!
      Last edited by lewewoo; 11-07-2011, 07:17 PM.

      Comment


      • #4
        Have you solved the problem? I have the same problem with you. Please help us!!!!!

        Comment


        • #5
          my solution is waiting....if the terminal window is still working, do nothing just wait.... other samples only 2hours, this sample needs overnight...dont know why .... good luck!

          Comment


          • #6
            I also tried cufflinks and it also stops. When I leave it and waited it, there will be "processing stop" appeared on the terminal. Do you see this problem?


            Thanks!

            Comment


            • #7
              no, i did not see that, can you post all the command and response message here? maybe can know what happened...

              Comment


              • #8
                Hi,

                Obviously this thread is quite old, but if experiencing a similar problem you might want to try the patch (and patched binaries) described here: https://groups.google.com/forum/#!to...rs/UzLCJhj3lUE

                Please let me know if this resolves the situation!

                Chris

                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