Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Issue with Randfold p-value in mirdeep2 for non model organism.

    Hello,

    I am facing a challenge with the output of mirdeep2 for non model organism with not previously identified microRNAs. Since my organism of interest has no previously identified microRNAs, I understand that I can use mature microRNA of genetically closer organism to mine. However, when I run this, all the microRNAs identified have a Randfold p-value 'no' suggesting that all those microRNAs predicted in my organism are not real. I think there is problem somewhere which I cannot point at. My script for running this is:

    mapper.pl A.fastq -e -h -i -j -l 18 -r 5 -m -p ./A_index/Amm -s A_collapsed.fa -t A-reads_vs_refdb.arf -v -o 16

    then
    miRDeep2.pl A_collapsed.fa A.fasta A_collapsed_vs_genome.arf none miRBase_dme_v14.fa none 2>A_report.log

    Any suggestion here will be appreciated.

    NOTE: I had run another analysis on a different organism with some microRNAs already identified, and the results were fine. Am not sure what is going on in this new one. Any help please.

    Erick

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