Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Hisat2 vs Tophat2 variation between tech reps

    I have a question regarding the variability of FPKM I am seeing between technical replicates in the Hisat2, stringtie pipeline. When I plot technical replicates by log2 FPKM, I am getting Spearman correlations of 0.6. I used the same fastq files in the tophat, cufflinks pipeline (default settings) and had Spearman correlations of 0.9. I am wondering which parameters I can change in Hisat2 to make it behave more like tophat2. In hisat, I have tried several different parameters and I am getting similar results regardless of the parameters I use.

    The parameters I have tried in hisat2 are as follows:

    -k 2 --max-seeds 15 --no-mixed

    -k 3 --max-seeds 10

    -k 10 --max-seeds 10

    default settings


    I am getting a high percentage of multi-mapping (~20%) and I am wondering if that is a problem.

    Thank you for your help!

  • #2
    I have answered my own question, but I am posting just in case someone else has a similar issue.

    I ran the same tophat data with stringtie and got a similarly bad correlation between technical replicates of 0.62. Now I know that the problem must be with stringtie and not with hisat2.

    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
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 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