Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Help with determine a closer-related genome

    Hi,

    I have a set of Illumina Hiseq 2000 bacteria transcriptome data set. From NCBI, I noticed that they have 2 same species but different strain genome sequence is available.

    I decide to choose a closely related genome for my bacteria transcriptome data set as a genome-guide assembly.
    Can I know how I determine which available genome is more closely related to my data set?

    I have try to map the clean read of my bacteria transcriptome data set against those 2 genome separately.
    It shown 97% of baceteria transcriptome read map to genome A (genome size is 4Mb) and 96% of bacteria transcriptome read map to genome B (genome size is 3.8Mb).
    It seems like my reads map more in genome A than B.
    But genome size of A is slightly larger than B.
    I not sure whether more reads map to genome A is due to larger genome size in genome A.

    Thanks for any advice that able to determine which genome is more closely related to my bacteria transcriptome data set.

  • #2
    Map reads to genome A as you did. The unused reads, map those to genome B. Do they map? Where and what genes?

    Do the same with B, map to B, use unused reads to map to A, do they map? where?

    Also, you got 2 strains of a bacteria, it is very likely that there is some significant difference between both. Perhaps an extra gene, or perhaps polymorphisms between the rRNAs. Look for those. Once you find something, look at your reads, which polymorphisms they have.

    Comment


    • #3
      Hi AdrianP,

      Many thanks for advice.

      I will have a try based on your suggestion.
      It is very useful for my research.
      I have a try on it now.
      Let you know once result is ready.

      Thanks again, AdrianP.

      Comment

      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, 03-27-2024, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      69 views
      0 likes
      Last Post seqadmin  
      Working...
      X