Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Target prediction between complementary RNA-seq and Small-RNA-seq data sets

    Hi everyone-

    Short background: I have Illumina sequence data on mRNA and microRNA from the same samples. Theoretically these two separate lists of sequences should contain complimentary microRNAs and mRNAs. I have no reference genome for my species however many of my microRNAs match to already annotated sequences from related species on miRBase along with a few potential novel microRNAs.

    Question: Does anyone know if it is possible to datamine these two profiles and predict mRNA-microRNA targets from de novo assembled transcriptome data? There seem to be many programs that utilize reference transcriptome data but I am not interested in that since I have assembled the transcriptome for my species de novo from the mRNA RNA-seq data.

    I'm not sure if I can use de novo assembled transcriptome data for microRNA target prediction through already existing programs; I currently have a subscription to CLC genomics workbench which appears unable to do so. This could potentially require the development of a custom script... Any information would help!

    Thanks!

    arom2

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
30 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
201 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
212 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
194 views
0 likes
Last Post seqadmin  
Working...
X