Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Hello I'm from Mexico

    I'm a masters student of biochemical sciences.

    I have some questions: is posible know the genome size by NGS? and if it's posible how much do you need to sequence to have a good estimate?

  • #2
    Hello ppbto,

    You should ask your question in the bioinformatics forum instead of the Introductions one. Anyhow, as I understand it your question is:

    Is it possible to estimate the genome size only by using HTS data? If it is possible, what sequencing depth do you need to obtain an accurate estimate? 2x? 4x?

    Greetings,
    Leo
    L. Collado Torres, Ph.D. student in Biostatistics.

    Comment


    • #3
      Hello again,

      Check the paper on the Panda genome http://dx.doi.org/10.1038/nature08696 . It doesn't answer your question completely, but it's a start.

      To assess genome coverage of the assembled contigs and scaffolds,
      we first estimated the genome size of the panda. To obtain the best
      estimate, we used sequencing depth, size ratio of syntenic blocks, and
      comparison of C-values. Using 17-base oligonucleotides and their
      frequency distribution in the usable sequencing reads to determine
      sequencing depth11, we obtained an estimated panda genome size of
      2.46 Gb (Supplementary Fig. 8). Given the presence of sequencing
      errors, we expect that the sequencing depth is underestimated, and
      consequently the panda genome size should be slightly smaller than
      2.46 Gb.
      Greetings,
      Leo
      L. Collado Torres, Ph.D. student in Biostatistics.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        by seqadmin


        The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist on Modified Bases...
        Today, 07:01 AM
      • seqadmin
        Current Approaches to Protein Sequencing
        by seqadmin


        Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
        04-04-2024, 04:25 PM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 04-11-2024, 12:08 PM
      0 responses
      37 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 10:19 PM
      0 responses
      40 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-10-2024, 09:21 AM
      0 responses
      35 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 04-04-2024, 09:00 AM
      0 responses
      54 views
      0 likes
      Last Post seqadmin  
      Working...
      X