Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • ParthavJailwala
    started a topic Cuffmerge related query

    Cuffmerge related query

    I have a query regarding what samples should be merged using cuffmerge, when you have multiple phenotypes (each with replicates). Lets say my mouse dataset comprises of one set of RNA-seq samples resulting from mutation of gene X, while there is another set resulting from mutation of gene Y. So the samples are:

    Samples:
    GeneXmutation (3 reps)
    GeneYmutation (3 reps)
    B6ctrl (3 reps)
    MixedCtrl (3 reps)

    The cuffdiff comparisons of interest are:

    Phenotype A: GeneXmutation (3 reps) vs B6ctrl (3 reps)......[GeneX mutation is on the B6 background]
    Phenotype B: GeneYmutation (3 reps) vs MixedCtrl (3 reps)....[GeneY mutation is on the Mixed background]

    I have the cufflinks assemblies for each of the 12 samples. My question is: should the cufflinks assemblies (transcripts.gtf) of all the samples above be merged one time using cuffmerge (all 12 samples as above) OR I should be running two cuffmerges: one for Phenotype A comparison and other for Phenotype B comparison? Does one approach over the another make a huge difference?

    Thanks

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 06:53 AM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
31 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
203 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
212 views
0 likes
Last Post seqadmin  
Working...
X