Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • deanie
    replied
    Thanks gringer. It does seem a little grey compared to other examples of technical and biological replicates I've seen. I expect the biological variation to be limited as it is a blood sample taken at once (i.e. fingerprick and three 10ul samples taken).

    Leave a comment:


  • gringer
    replied
    It is a type of technical replicate, but will have some degree of biological variation from the different samples. Usually "technical replicate" refers to an additional sequencing library prepared from the same extract.

    In this case because there is a chance of biological variation, I would keep the samples separate and add the sample as an additional factor in any statistical models.

    Leave a comment:


  • deanie
    started a topic Dealing with technical replicates

    Dealing with technical replicates

    First question, can anyone confirm these are indeed technical replicates?

    3 blood samples taken from the same individual, each processed separately and final libraries pooled for sequencing (paired-end). So have a pair of fastq files for each of the replicates.

    Second question, what are your opinions on how to deal with the technical replicates during differential expression analysis?

    I've heard of technical replicates sequenced over different lanes and then combining the fastqs. In this lab's experiment there is no lane variation due to the multiplexing. Is it still sensible to combine them in the case described above?

    Or separately process the fastqs for each replicate (i.e. qc, trimming, counts) and then combine the read counts? Based on what I read most people sum the counts of the technical replicates, with a few posts suggesting averaging them.

    TIA!

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
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X