Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Identifying antisense transcript with stranded mRNA-seq.

    Hello to all,

    I have one dataset that contains samples (2 conditions in 2 replicates) sequenced with "TruSeq Stranded mRNA Sample Prep Kit" : directional mRNA-seq.

    How is it possible to study the antisense transcripts? In fact, I have theoretical and technical questions about it.

    - antisense transcripts have as template the sense strand of DNA (and thus have the same sequence as the antisense strand of DNA) ? So antisense transcripts are transcribed from + strand ? and conversely, sense transcripts have as template the antisense strand of DNA (and thus have the same sequence as the sense strand of DNA) ?

    - when I align my data with the TopHat tool (with fr-firstrand option, because this is a dUTP protocol), I have a XS:A tag by read, following by + or -. So, reads that are tagged by XS:A:+ correspond to sense transcripts and reads that are tagged by XS:A:- correspond to antisense transcripts ?

    - in this topic "http://genomebytes.wordpress.com/2013/07/08/fixing-the-xs-tag-in-tophat-output-bug-fixing/", Chung-Chau Hon said : "If a read is mapped on a feature specified in the GTF, the XS tag would always be on the same strand of the feature not matter what strand the read is mapped to. This would create wrong counts is there are unannotated antisense transcripts.". How do you study these antisense transcripts?

    Thank you in advance for your response.

Latest Articles

Collapse

  • 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
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
25 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
24 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
52 views
0 likes
Last Post seqadmin  
Working...
X