Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #46
    Originally posted by colaneri View Post
    DESeq needs count data in the form of rectangular table. My question is whether is correct or possible to use the genes.count_tracking file generated with cuffdiff as the counts table that DESeq requires?
    It is not correct, but it is possible to force DESeq to accept it. DESeq expects raw read counts, not normalised counts, as in the count_tracking files. As a warning, DESeq will complain if you try to feed it decimal values in the data table -- this is an indication that you're doing something you shouldn't.

    If you're using cuffdiff to get the count data, why not use it to do the differential analysis as well?

    Comment


    • #47
      combining tophat with DESeq

      Originally posted by gringer View Post
      It is not correct, but it is possible to force DESeq to accept it. DESeq expects raw read counts, not normalised counts, as in the count_tracking files. As a warning, DESeq will complain if you try to feed it decimal values in the data table -- this is an indication that you're doing something you shouldn't.

      If you're using cuffdiff to get the count data, why not use it to do the differential analysis as well?
      The reason is because I'm comparing the response of two genotype to two growing conditions, and I want to study the interactions of genotype x treatment

      When using cuffdiff I just obtain a comparison of everything against everything. But most of that comparison are not usefull. DESeq can to two factor analysis.

      The problem is I do not know how to create the entry table with good metadata about gene information, that is what I was thinking in use the gene.count tracking file. I like how tophat align the sequences also.

      But now regarding what you told me of decimal numbers. I'm not talking to feed DESeq with RFPK values. It look to me that the gene.count traking files contains the raw number of reads mapped to each gene

      Comment


      • #48
        Aren't the counts in the gene.count_tracking file scaled (i.e. they can be decimal)? Normally, one would just use htseq-count to generate a count table for DESeq. That's the simplest way to go about things and then you can easily check if the raw counts do in fact match those in the gene.count_tracking file.

        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
        24 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        25 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        52 views
        0 likes
        Last Post seqadmin  
        Working...
        X