Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cuffcompare only generates .gtf.tmap and .gtf.refmap?

    Hi all,

    I've been able to run a tophat/cufflinks with no prob. However, when I run cuffcompare, it only gives me the .gtf.tmap and .gtf.refmap files with no <outprefix>, <outprefix>combined.gtf, and <outprefix>.tracking files.

    My cuffcompare command looks something like this.

    cuffcompare -V -r blabla.gff -s blabla.fa tanscripts_1.gtf transcripts_2. gtf and so on...

    Anyone ever encountered this issue?
    Cheers,

  • #2
    i just got the same situation. have you resolved this problem??

    Comment


    • #3
      Unfortunately no. I haven't try to solve this issue since a couple of months though. I'm wondering if it has to do with the fact that I am comparing samples with no replicates... Are you trying Cufcompare with replicates?

      Comment


      • #4
        yes, data i use have replicates.

        Comment


        • #5
          and each of the lanes correspond to a pooled sample of 5-6 replicates.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM
          • 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

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          17 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          22 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          46 views
          0 likes
          Last Post seqadmin  
          Working...
          X