Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • miRNAkey

    Hi All,

    I am referring to your publication "miRNAkey: a software for microRNA deep sequencing analysis" in Bioinformatics.

    I have few questions regarding the output of the miRNAkey. Specifically I am referring to an Excel file for Differential Expression Table. For most of miRNA, there are two rows (for examples hsa-let-7a and hsa-let-7a*), what is the difference between these two miRNA? Also, it generates fold-change value of +Infinity for positive two number (for example fold-change for RPKM1=0.801 and RPKM2=591.740 is +Infinity). Is it possible to convert mapped .sam file to .bed format to visualize the data in the UCSC genome browser?

    I really appreciate your help on these issues.

    Thanks,

    Rakesh

  • #2
    A microRNA is processed from a precursor miRNA (pre-miR). From a pre-miRNA, two miRNA are processed, the mature and the star.

    So hsa-let-7a and hsa-let-7a* are processed from the same pre-miR (http://www.mirbase.org/cgi-bin/mirna...?acc=MI0000060).



    To convert .sam to .bed --> http://seqanswers.com/forums/showthread.php?t=2446

    For the foldchange, I don't use miRNAkey..

    Nico

    Comment


    • #3
      Hi Nico,

      Thanks for your detail response. I tried to use samtools and bedtools to convert .sam files to .bed files but I used human genomes 19 as reference. But I believe it might be better to use miRBase instead. Do you have any other suggestions?

      Best wishes,

      Rakesh

      Comment


      • #4
        miRNAkey error

        Alignment summary:
        Total reads: 736516
        Mapped reads: 255576
        Uniquely mapped reads: 249567 (97.6% of mapped reads)
        Multiply mapped reads: 6009 (2.4% of mapped reads)


        Error message:
        .....
        Use of uninitialized value in concatenation (.) or string at /downloads/miRNAkey/pipeline/make_multi_input.pl line 181, <$BWA_INPUT> line 738143.
        Use of uninitialized value in concatenation (.) or string at /downloads/miRNAkey/pipeline/make_multi_input.pl line 200, <$BWA_INPUT> line 738143.
        .....
        Differential Expression Analysis summary:
        A total of 2 different miRNAs were expressed in the two samples


        its the same error at line 181 and 200 for all the samples ; and all samples show only two differentially expressed miRNAs

        (i tried with Bwa.0.5.7 and 0.5.9 ): both has same errors

        please do suggest me what went wrong and how to over come this error?
        Last edited by gpcr; 03-28-2012, 09:13 AM.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Quality Control Essentials for Next-Generation Sequencing Workflows
          by seqadmin




          Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

          Nucleic Acid Quality Control
          Preparing for NGS starts with isolating the...
          02-10-2025, 01:58 PM
        • seqadmin
          An Introduction to the Technologies Transforming Precision Medicine
          by seqadmin


          In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
          01-27-2025, 07:46 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 02-07-2025, 09:30 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-05-2025, 10:34 AM
        0 responses
        104 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-03-2025, 09:07 AM
        0 responses
        83 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 01-31-2025, 08:31 AM
        0 responses
        45 views
        0 likes
        Last Post seqadmin  
        Working...
        X