Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Pair-end sequences assembly with Trinity (data mining doubt)

    Hello everyone, I'm a Master student from Spain and this is my very first job with bioinformatics and RNA-Seq, so please excuse me if my questions are too easy or are not very clearly explained.

    I have two files containing 100pb pair-end reads from Illumina RNA-seq and I want to assembly them into a De Novo transcriptome using Trinity. Up to here everything is OK, but I have some doubts about the process of combining the two files (containing the F and the R reads) to obtain a “consensus” sequence for the k-mer dictionary construction and the downstream processes (actually I don’t really know if such a “consensus” sequence is formed or not when you perform the Inchworm algorithm of the assembly).

    My main doubt is if the F and the R reads of the 100pd fragment need to be of the same length. I wonder this because the first 9-10 bases of each read have poor per sequence position quality, and if I trim them I don’t know if it’s going to be a disaster (because I don’t know if Trinity align the F and R reads or if it just transforms the R reads to their reverse complementary and obtains the k-mers from the F and the R-transformed reads independently).

    I know it’s a bit messy but I will be very grateful if anyone can help me

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
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
50 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X