Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • OLB 1.6.1 vs 1.8.0

    Hello all,

    We started using OLB-1.8.0 last week, I've been running some tests. For genomic samples it looks great, an increase in clusters detected, but same high pass filter & mapping rates. However for mRNA & CHiP-Seq samples I'm seeing a decrease in called clusters for half the samples -- has anyone else noticed this? I'm wondering if 1.8.0 is something we should only be using for genomic and stick to 1.6.1 for other types of samples...thoughts?
    Christine Brennan
    UM DNA Sequencing Core
    Ann Arbor, MI 48109

    [email protected]

  • #2
    The only thing we noticed when doing comparisons of 1.8 and 1.6 was that when cluster density was below 200,000 clusters per tile (~350,000 clusters/mm2) that there was either a small increase or a decrease in the number of reads. In all samples with a higher density, we saw at least a 10% increase, including RNA and ChiP-seq samples.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Exploring the Dynamics of the Tumor Microenvironment
      by seqadmin




      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
      07-08-2024, 03:19 PM
    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      06-25-2024, 06:43 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:53 AM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    34 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 09:45 AM
    0 responses
    204 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 08:54 AM
    0 responses
    213 views
    0 likes
    Last Post seqadmin  
    Working...
    X