Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • RNA-Seq: DEB: A web interface for RNA-seq digital gene expression analysis.

    Syndicated from PubMed RSS Feeds

    DEB: A web interface for RNA-seq digital gene expression analysis.

    Bioinformation. 2011;7(1):44-5

    Authors: Yao JQ, Yu F

    Abstract
    Digital expression (DE) is an important application of RNA-seq technology to quantify the transcriptome. The number of mapped reads to each transcript or gene varies under different conditions and replicates. Currently, three different statistical algorithms (edgeR, DESeq and bayseq) are available as R packages, to compare the reads to identify significantly expressed transcripts or genes. So far, users have to manually install and run each R package separately. It is also of users' interest to compare the results of different approaches. Here, we present a pipeline DEB which automates all the steps in file preparation, computation and result comparison. AVAILABILITY: The database is available for free at http://www.ijbcb.org/DEB/php/onlinetool.php.


    PMID: 21904439 [PubMed - in process]



    More...

  • #2
    I have tried it, no results after >3 days.

    Comment


    • #3
      Originally posted by mosalem View Post
      I have tried it, no results after >3 days.
      Me too, it takes such a long time or there is no result!
      Engineer of Data Analysis
      E-mail: [email protected]

      Comment


      • #4
        I am in the same boat. It takes a very long time for relatively large data/file. But using only the first 60 genes of the example/demo data, i get the result after about 3 mins (choose only one algorithm). Could the authors or anybody give us some ideas or solutions? Thanks.

        Comment


        • #5
          Using there Demo file works. But no luck with my file. Just tries forever and no error message.

          Comment


          • #6
            Same problem, demo files work, but impossible to get results with my data. Someone had a DEB answer?

            Comment


            • #7
              No, I've tried it several times and it has never worked. Actually just writing an R script that calls edgeR, baySeq and DESeq takes about 10 minutes if you follow the respective vignettes, so I've realized this web interface is rather pointless ...

              Comment

              Latest Articles

              Collapse

              • 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
              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 06:37 PM
              0 responses
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              49 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              66 views
              0 likes
              Last Post seqadmin  
              Working...
              X