Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • miRDeep2

    Hello,

    I Am currently using miRDeep to to analyze small RNA-seq data from the Solid 4.

    However I am having trouble aligning expression between samples.

    Does anyone have experience with miRDeep that could suggest a method or suggest another mapping/analysis program.

    Thanks,

    Anthony

  • #2
    what do you mean by aligning expression ? the reads ?

    Comment


    • #3
      sorry I was not more clear.

      I mean aligning the reads for each microRNA from different samples. The output does not lend itself to that as far as I can figure out. Just wondering if others had encountered this problem and figured out how to solve it.

      Comment


      • #4
        Hi,

        I am trying to identify miRNA from fastq file. I am using miRDeep2 for this purpose. As mentioned in the in the tutorial regarding the mature and precursor sequences of miRNA, I have downloaded it from miRBase version 21. While running the mirdeep2.pl command im getting this error in the report.log file.

        " #Starting miRDeep2 /home/titan4/mirdeep2_0_0_8/src/miRDeep2.pl reads_collapsed.fa hg38.fa reads_collapsed_vs_genome.arf mature_new.fa none precursor_new.fa -t H.sapiens

        miRDeep2 started at 12:3:54

        mkdir mirdeep_runs/run_24_06_2016_t_12_03_54
        testing input files

        started: 12:3:54 sanity_check_mature_ref.pl mature_new.fa

        Error: problem with mature_new.fa Error in line 5.177: The sequence



        contains characters others than [acgtunACGTUN]

        Please check your file for the following issues:

        I. Sequences are allowed only to comprise characters [ACGTNacgtn]. II. Identifiers are not allowed to have withespaces.

        Can some one help.

        Comment


        • #5
          It looks like you likely have whitespaces in the headers of your fasta file, which mirDeep does not allow. See https://www.biostars.org/p/135035/ for various options on how to remove these

          Comment


          • #6
            Novel MicroRNA prediction with Mirdeep 2.

            I recently done small RNA sequencing of my endocrine tumour samples. I got result analysis with Mirdeep2 . I am not master in bioinformatics so , i outsourced the analysis. The company have predicted some novel micrornas. They have used mirdeep2 software for predicting novel microRNA.

            I am facing problem in selecting novel microRNAs from small RNA sequencing. Is it necessary to have high mirdeep2 score with high mature read count. Those sequence with high mirdeep2 score ( like 3168) & mature read count (456) have non significant RANDFOLD p value. I am confused in this part.

            I read in mirdeep2 documentation in which the score cut was from -10 to 10.but i am getting mirdeep2 score of like 200 , 361. I am really very confused. Then i started comparing total read length , loop read length. But still confused.

            Please guide me regarding mirdeep2 software and please help me its parameters for selecting novel microRNA.I will be very thankful to you.

            Comment

            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
            12 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-27-2024, 06:07 PM
            0 responses
            11 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
            68 views
            0 likes
            Last Post seqadmin  
            Working...
            X