Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cufflinks / cuffcompare does not produce p_id

    Hello,

    My first post here...!

    I'm trying to use cuffcompare to produce a combined GTF file (stdout.combined.gtf) to feed to cuffdiff for further analysis. Cuffcompare should produce such GTF with added attributes tss_id and p_id. However, while my stdout.combined.gtf does have tss_ids it has no p_ids (even if the input file has CDS attributes). How is it?
    I guess I can put the p_ids myself, but I'd like to understand what I'm doing wrong.

    As a test, I ran cuffcompare using the pig GTF from ensembl against itself (following a trick from Cole Trapnell I found in another post) and indeed I couldn't 'see' any p_id in the output. See script below to reproduce this test.
    Why I don't get p_ids?! Am I missing something very obvious?

    I'm using version cufflinks-0.8.2.Linux_x86_64

    Thanks in advance for any help!
    Dario

    Here's the little code:
    # -----------------[ Cut here ]---------------------

    ## Download and unzip pig GTF
    wget ftp://ftp.ensembl.org/pub/current_gt...ofa9.57.gtf.gz
    gunzip Sus_scrofa.Sscrofa9.57.gtf.gz

    ## Run cuffcompare
    /exports/work/vet_roslin_nextgen/dario/cufflink/current/cuffcompare -r Sus_scrofa.Sscrofa9.57.gtf Sus_scrofa.Sscrofa9.57.gtf Sus_scrofa.Sscrofa9.57.gtf

    ## No p_ids!!
    grep p_id stdout.combined.gtf
    ==> no hits

    # ----------------------[ Cut here ]-----------------

  • #2
    The trick I posted apparently doesn't always work - we know about this bug and will address it in an upcoming release

    Comment


    • #3
      Originally posted by Cole Trapnell View Post
      The trick I posted apparently doesn't always work - we know about this bug and will address it in an upcoming release
      Hi Cole et al.,

      Thanks for taking time to reply.
      Is the bug due to some anomalies in the GTF file? If so, would it be possible to post a few lines from a GTF that works? A final question if you can answer... even if this bug occurs, are the other results from cuffdiff reliable? (I'm not interested in running the reference GTF against itself, that was just for testing purposes).

      Dario

      Comment


      • #4
        We think they're reliable

        The bug I mentioned is just in cuffcompare's ability to attach p_id attributes automatically. If the p_id attributes are missing, Cuffdiff will simply not perform a CDS-level differential analysis. It will look for changes in splicing and TSS preference (and of course gene and isoform-level expression), but it won't look for changes in coding output.

        Comment


        • #5
          Originally posted by Cole Trapnell View Post
          We think they're reliable

          The bug I mentioned is just in cuffcompare's ability to attach p_id attributes automatically. If the p_id attributes are missing, Cuffdiff will simply not perform a CDS-level differential analysis. It will look for changes in splicing and TSS preference (and of course gene and isoform-level expression), but it won't look for changes in coding output.
          Cole,

          Did you fix this bug?
          I am running a Cuffdiff on two pig samples and ended up with Segment error. I then checked the combined_transcript.gtf file generated in Cuffcompare but did not find the p_id. By the way, I am using the cufflinks .8.4 version released 16/7/2010

          Thanks a million!

          jhuang

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM
          • seqadmin
            Recent Advances in Sequencing Analysis Tools
            by seqadmin


            The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
            05-06-2024, 07:48 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 05-24-2024, 07:15 AM
          0 responses
          93 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 10:28 AM
          0 responses
          105 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 07:35 AM
          0 responses
          106 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-22-2024, 02:06 PM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Working...
          X