Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
This topic is closed.
X
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • David R
    started a topic Introduction and TnSeq

    Introduction and TnSeq

    Hi everyone , it has been a while since I las posted here. So long I had to sign up anew (new mail etc.) Nice to be back. Still interested in NGS analysis. I hope you may help me. I have to analyze some TnSeq data. Since I am quite new to this kind of data, I would like to post here a couple of questions, one more “conceptual” than the other. I hope this forum is suitable for this.
    1- Why do we tend to analyze TnSeq data as ZINB-distributed data? What is it so different from RNASeq? I understand that in TnSeq there are loads of zero counts and, crucially, we do not know where those zeros come from, i.e. we do not know if it is a zero because (i) a given TA site has not been used in the library or (ii) because the gene is “essential” and, therefore, mutants with insertions in that genes have not survived. In RNASeq we also have loads of zeros, and we do not know if that is because the gene is not expressed or because the sample has not been sequenced deep enough. Therefore, I cannot tell the difference, to be honest.
    2- Regarding practical issues. I know there is TRANSIT in Python to analyze TnSeq data, including multifactorial designs (which is my case). However, I have not seen similar tools in R. Am I wrong?
    Thanks a lot for any help or hints on those two questions.
    Best regards,
    David R.

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, Today, 06:53 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
30 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
202 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
212 views
0 likes
Last Post seqadmin  
Working...
X