Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • samtools faidx

    Hi,

    I've aligned RNA-Seq PE reads to X.laevis unigene EST database and have generated DE gene lists with cuffdiff. I assumed that there was no annotation file but have just noticed that the .fa file contains annotation in the scaffold (expressed gene) name. For example:

    gnl|UG|Xl#S14232313 Xenopus laevis hypothetical protein MGC52983, mRNA (cDNA clone MGC:52983 IMAGE:4930778), complete cds /cds=p(53,1054) /gb=BC046667 /gi=28302290 /ug=Xl.7 /len=18
    91

    However, when I use this .fa file for cufflinks/cuffdiff only the first part of the name gets carried over as 'gene' column in the cuffdiff output file gene_exp.diff. e.g.

    gnl|UG|Xl#S28473480:69-1962

    Is there any way to ensure the entire name gets carried over to help make sense of the gene lists generated in cummerbund?


    Any help would be very welcome!

    Best,

    N

  • #2
    Just replace all of the spaces with underscores.

    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, Yesterday, 12:08 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    14 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    43 views
    0 likes
    Last Post seqadmin  
    Working...
    X