Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • RNA-seq analysis

    I am doing RNA seq analysis for different gene expression analysis. I find that people use two approaches:

    1. Tophat - HtSeq - edgeR or DESeq R package
    2. Tophat - Cufflinks -Cuff Diff

    which approach that your guys use most? any advice?

  • #2
    I am in an early phase of my RNA-seq project and by now I'm using DESeq and edgeR for estimating modulated genes (DEG) and cufflinks /cuffcompare/cuffdiff for exploring differentially expressed transcripts, differential splicing and differential promoter use.

    if I also use cufflinks for estimating DEGs, I usually get some 50% DEGs in common with DESeq. DESeq and edgeR, on the other hand, share 80% of estimated DEGs.
    I am still experiencing things but I guess that the % of common DEG between DESEq and cufflinks is very much influenced by how you run cufflinks (reference GTF or not and other parameters as -R when running cuffcompare).
    I didn't try the latest cufflinks version yet, however. I used version 0.9.3

    It would be nice getting inputs on what others are doing !
    hope it helps,

    pbseq

    Comment


    • #3
      Just wanted to let you know that Cufflinks 1.0 has a completely revamped approach to DE that models over-dispersion of counts at the transcript level and we'll be curious to know how it performs on your tests.

      Comment


      • #4
        lpatcher,
        for sure I'll try soon latest version of cufflinks !

        Comment


        • #5
          Hello,

          I want to analyze my RNASeq data using DESeq. Would anyone tell me how and where to find codes for DESeq? Thx

          Comment


          • #6
            What do you mean by "codes"?

            We have written a nice manual (a "vignette") for DESeq, which you find here. We are currently overhauling it, and you'll find the improved vignette soon here.

            Comment


            • #7
              Thank you Simon.

              Comment


              • #8
                Hi Simon, how can I get TagSeqExample.tab file for practice?

                Comment


                • #9
                  I got it

                  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
                  25 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 04-10-2024, 10:19 PM
                  0 responses
                  28 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 04-10-2024, 09:21 AM
                  0 responses
                  24 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