Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cuffdiff with more than two samples

    Recently,I'm using Cufflinks to process my RNA-seq data,and I have 4 tissues(more than two).In the mannual of cuffdiff,you said,if more than two are provided, Cuffdiff tests for differential expression and regulation between all pairs of samples. But when I used the cuffdiff,it only report one pairs of samples.There was only one gene_exp.diff in the output directory.Command was just as below,
    ======================================
    cuffdiff -o DEG_cuffdiff -p 20 cuffcmp.combined.gtf ./tophat_sd/accepted_hits.bam ./tophat_em/accepted_hits.bam tophat_en1/accepted_hits.bam ./tophat_en2/accepted_hits.bam
    ======================================
    What's my problem in using cuffdiff?
    Also I want to compare gene expression of duplicate gene pairs, and is it neccesery to remove the reads that mapped to multiple location in the BAM file generated by Tophat as duplicate gene pairs have high sequence similarity ?
    Thanks!

  • #2
    For Question 1:

    Yes, Cuffdiff would only generate one output even though you have more than one comparisons. However, all other comparisons are also included in that file. Check the output file more carefully.

    Comment


    • #3
      I have checked the outpu directory.

      In fact, I have checked the outpu directory, and there are only 11 files as follows:cds.diff , cds_exp.diff,genes.fpkm_tracking, isoforms.fpkm_tracking ,splicing.diff, tss_groups.fpkm_tracking , cds.fpkm_tracking , gene_exp.diff isoform_exp.diff , promoters.diff , tss_group_exp.diff. And I did not find any other comparison files between genes.
      I have posted this problem on the other thread ,and his met the similar issue.
      Application of sequencing to RNA analysis (RNA-Seq, whole transcriptome, SAGE, expression analysis, novel organism mining, splice variants)

      Comment


      • #4
        I am not quite sure right now for your case. But I did this before and I can get all the comparisons. For example, if I open the gene_exp.diff file, I will have the q1 vs q2 first. And when I continue check the result by clicking pagedown, I will find q1 vs q3 and etc.

        Comment


        • #5
          Thanks for your help

          Now I know all of results of the comparisons betweem pairs are saved in one file.
          Thanks!

          Comment

          Latest Articles

          Collapse

          • 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
          • seqadmin
            Essential Discoveries and Tools in Epitranscriptomics
            by seqadmin




            The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
            04-22-2024, 07:01 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Today, 02:46 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-07-2024, 06:57 AM
          0 responses
          13 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-06-2024, 07:17 AM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-02-2024, 08:06 AM
          0 responses
          23 views
          0 likes
          Last Post seqadmin  
          Working...
          X