Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • one gene one RPKM cufflinks or DEseq

    Hi, guys, I need your expert input. So, I am not worried about the isoforms, at least for now. I just want to assign a rpkm for each gene. From what I read here, DEseq should get the job done.

    But I already have the cufflinks out and want to do something quick. Should I add the FPKM for different transcript or should I do something else? Thanks!

  • #2
    DESeq is for comparing genes across samples, not for calculating RPKM.

    Maybe you better first explain why you want RPKM values: what do you want to do with them once you have them?

    Simon

    Comment


    • #3
      Yes, you can add the FPKM for individual transcripts in a gene to get an overall FPKM.

      Comment


      • #4
        If I were to un-normalize these FPKMs in order to get the raw reads that cufflinks assigned to each gene... what would the M in FPKM normalization factor be - the total number of alignments produced by tophat, or the unique number of reads that mapped at least one time? Or just the number of reads that mapped to the actual features, i.e, genes?

        What subset of all the accepted_hits.sam file does cufflinks use to normalize the reads after accounting for transcript length?

        Thanks,
        Carmen

        Comment


        • #5
          Hi all, a question along the lines of the discussion:

          I made a table count with htseq-count then run edgeR. Now I have a table with GeneID, logFC, logCPM, LR, PValue and FDR. Now I would like to add RPMK values to this table.

          edgeR has an rpkm function (x, gene.length, normalized.lib.sizes=TRUE, log=FALSE, prior.count=0.25) but I know that figuring out 'gene.length' is a tough task (and I guess this is why is better to do transcript-based differential expression analysis as opposed to exon-based).

          So what would be a good criteria to select gene.length for an RNA-seq using TAIR10 (Arabidopsis)??

          Any ideas?

          thanks
          G


          Thanks All
          G

          Comment


          • #6
            Most people would just use a union exon model (i.e., add up the non-overlapping exons for each gene).

            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
            67 views
            0 likes
            Last Post seqadmin  
            Working...
            X