Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • What next after cuffDiff - isoforms

    Dear Loyal,

    thanks for the providing cummeRbund. I am enjoying this package every bit of it.

    I have one question when it comes to isoforms.

    I see that I have 702 isoforms.


    ###########################################
    CuffGeneSet instance for 669 genes

    Slots:
    annotation
    fpkm
    repFpkm
    diff
    count
    isoforms CuffFeatureSet instance of size 701
    TSS CuffFeatureSet instance of size 675
    CDS CuffFeatureSet instance of size 682
    promoters CuffFeatureSet instance of size 669
    splicing CuffFeatureSet instance of size 675
    relCDS CuffFeatureSet instance of size 669
    #############################################

    when I visualize them in IGV, for gene especially long genes my eyeballs pain and I get hypnotized by lines, to identify which exons are different, or where exactly the splicing is different between q1 q2.

    What should one do given these 701 isoforms:
    1. How to get which exons differ between q1 vs. q2
    2. How to know if expression difference between these two isoforms.
    3. How to visually focus on exons that contributed to isoform and splicing difference.


    I tried using plotTracks. I cannot see all samples lined up for an exon difference.


    Any help to resolve this issue will be greatly appreciated.

    Thanks again.
    Adrian.

  • #2
    Sorry for bumping this message.

    Could any member please share how they are using the isofom diff list from cuffdiff. How are you identifying what exon is differing between two isoforms and how are you visualizing the exonic changes.

    thanks again.

    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, Yesterday, 01:32 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-24-2024, 07:15 AM
    0 responses
    199 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    221 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    231 views
    0 likes
    Last Post seqadmin  
    Working...
    X