Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Size of the reference sequence for SAET

    Dear all,

    This is my first post to this extremely useful forum about NGS (congratulations to everybody, and specially to the creators and maintainers), so that I would like to introduce myself to the community. My name is Javier Forment, and I am the responsible (and the only member) of a Bioinformatics Core Facility at the Institute for Molecular an Cell Plant Biology (IBMCP, for 'Instituto de Biologia Molecular y Celular de Plantas', www.ibmcp.upv.es), a research center in Valencia, Spain, belonging to the Universidad Politecnica de Valencia (www.upv.es) and the Spanish Scientific Research Council (www.csic.es).

    I would like to use SAET (http://solidsoftwaretools.com/gf/project/saet/) to improve the quality of SOLiD data produced by the different research groups at the IBMCP, and have a question about the parameter providing the expected length of the sequence from which reads were sampled. In one case, this sequence is a not-yet-finished draft genome, so that it has a significant amount of N's in some regions of the scaffolds.

    So the question is: do I must include these N's in the reference sequence size? Does it really matters? (size with N's: 794 MB; size without N's: 721 MB)

    Thanks in advance and best regards,

    Javier.

Latest Articles

Collapse

  • seqadmin
    Understanding Genetic Influence on Infectious Disease
    by seqadmin




    During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.

    Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...
    09-09-2024, 10:59 AM
  • seqadmin
    Addressing Off-Target Effects in CRISPR Technologies
    by seqadmin






    The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality1. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes2. This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways3. Identifying the full range...
    08-27-2024, 04:44 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 06:25 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 01:02 PM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 09-18-2024, 06:39 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 09-11-2024, 02:44 PM
0 responses
14 views
0 likes
Last Post seqadmin  
Working...
X