Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DESeq2 for isoform level

    Hello,

    (1) I was wondering whether DESeq2 is appropriate to test for differentially expressed isoforms? If we have raw counts (on isoform level), can we treat them like gene expression levels and run DESeq2?

    (2) Another question and a more specific one is: my isoforms counts are actually the estimated outputs of eXpress (eff_counts). Here's the explanation:

    "The estimated number of fragments generated from this target in the sequencing experiment, adjusted for fragment and length biases. In other words, his is the expected number of reads from the experiment if these biases did not exist. This is the value recommended for input to count-biased differential expression tools."

    I'm assuming that this can't be used as an input to DESeq2 since it's corrected for some biases, is that correct? If so, then is there another package that can be used for this?

    (3) In fact, eXpress has another output (est_counts), explained as follows:
    "The estimated number of fragments generated from this target in the sequencing experiment."
    I'm guessing this is the actual estimated counts, without any bias correction ... would this be appropriate for isoform-level DE analysis with DESeq2?

    Thanks in advance for any sort of comment and suggestion!

    Golsheed

  • #2
    hi Golsheed,

    The question about isoform counts has been asked and answered many times on Seqanswers and elsewhere, here is one of Simon's answers: https://support.bioconductor.org/p/43395/#43400 . DESeq2 is only designed for gene-level analysis.

    Comment


    • #3
      DESeq isoform level

      Thanks a lot for helping, Michael.
      (1) I guess the reason I got confused was that after reading Simon's answer, I also read this one:

      What are your thoughts on this? Since the corrected counts that I have at hand are from the output of the eXpress software, would this change your answer?

      (2) If not, would it be wrong to simply use a linear model to detect differential isoform expression, with the corrected counts I have at hand from eXpress? or does it have to be done with some of the available packages from scratch?

      I appreciate your help very much,
      Golsheed

      Comment


      • #4
        In my answer there, I am saying that the uncertainty of the isoform-level estimates from assigning shared reads is not passed through in the value, so we don't recommend this use for DESeq2. The Huber group does have DEXSeq for detecting differential splicing, using raw counts. There are plenty of methods and I'm not the one to say which you should use, other than to advise against isoform-level analysis with a gene-level tool.

        Comment


        • #5
          Makes sense. Thanks a lot for always being helpful.

          Golsheed

          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,”...
            Yesterday, 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, 07:15 AM
          0 responses
          12 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 10:28 AM
          0 responses
          15 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 07:35 AM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-22-2024, 02:06 PM
          0 responses
          9 views
          0 likes
          Last Post seqadmin  
          Working...
          X