Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Can I put single and pair-ended RNAseq data together in DESeq analysis

    I have RNA-seq data from Illumina GA (single-ended)and Hiseq (pair-ended). Just wonder if I could put them together in differential gene expression analysis. I know pair-end is much better than single-end in accuracy. But not sure if it is reasonable to put them together in the analysis. many thanks

  • #2
    No, paired-end is not better in accuracy. At least, for simple differential expression analysis, it does not make much of a difference.

    As for your question, the answer is: It depends.

    Hence, please always give details on your experimental design when posting a question here,

    Comment


    • #3
      Thank you for reply.
      I have 10 samples in treatment and 12 samples in untreatment group. In treatment, I have 5 single and 5 pair-ended samples. In untreatment, I have 8 single and 3 pair-ended samples.
      Sorry, I am not the person who designed the experiment. Have no idea why they put it into such way. But I have to do the data analysis.

      Many thanks.

      Comment


      • #4
        Well, as long as you have both platforms in both conditions, this is fine. Just treat the library type as a covariate, as in the example in the vignette. (There, we used on purpose a dataset with such a mixture of single-end and paired-end data to demonstrate how to use covariates.)

        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,”...
          05-24-2024, 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, 05-24-2024, 07:15 AM
        0 responses
        198 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 10:28 AM
        0 responses
        220 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 07:35 AM
        0 responses
        229 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-22-2024, 02:06 PM
        0 responses
        13 views
        0 likes
        Last Post seqadmin  
        Working...
        X