Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • rDNA and RNA-Seq

    Hello,

    I am currently analyzing sequencing data of total RNA from mouse samples. As can be expected in total RNA, I have quite a bit of ribosomal sequences. However, when aligning to my genome assemblies, I noticed that a very large amount (half of my total reads) were unmapped, and that almost all of them were easily mapped to "TPA: Mus musculus ribosomal DNA, complete repeating unit" using BLAST. This is where I get confused:

    - According to the literature I've consulted, rDNA is composed of a multitude of tandem repeats of the above-linked sequences. However, that sequence itself is not present even once in any of the genome assemblies (cattle, mouse) that I use on a regular basis, despite the gene having been clearly identified, sequenced, and even mapped to specific chromosomes using argent staining. Why is that?
    - Furthermore, what Is present within the genomes are repetitive sequences labeled "SSU-rRNA_Hsa" and other similar sounding names, but which are not organized in the way Nucleolar Organizer Regions (NOR) are supposed to be. Are these supposed to be inert or active copies of the rRNA genes?
    - And, more practically, should I add the rDNA sequences to the bowtie2 indices I use for my alignments?

    Thansk a lot for any help!

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