Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • tophat: definition of spanning mate pair

    I have found a reference where the "encompassing" read and "spanning" reads are being clearly distinguished and well defined.



    "Encompassing mate pairs refer to those in which
    each read aligns to an independent transcript, thereby encompassing
    the fusion junction. Spanning mate pairs refer to those in
    which one sequence read aligns to a gene and its mate spans the
    fusion junction."

    However, using tophat has been very confusing with no clear definition or figures to explain the wording.

    On tophat webpage, three types of reads are mentioned:


    "1. 106 is the number of reads that span the fusion,
    2. 116 is the number of mate pairs that support the fusion,
    3. 167 is the number of mate pairs that support the fusion and whose one end spans the fusion."

    Which one of the last two statements refer to encompassing and spanning mate pairs? Which out of 2 and 3 carries more weight? Any thoughts?

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
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
12 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