Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to decide the other arm in miRNA sequencing

    Hi,

    I am using your excellent software novoalign. my question is:

    when I use command: novoalign -d hg36.ndx -f s_1_0000_sequence.txt -a -m -l 18 -h90 -r A,

    I got report like:

    @SRR001342.63 S AAAATAAACAAATAGGG IIIIIIIIIIIIIIIII U 0 21 154 >gi|116010291 18213481 F . . .

    there are two possible precursor miRNAs

    5'----AAAATAAACAAATAGGG -------------- XXXXXXXXXXXXXXXXXX---

    5'---- XXXXXXXXXXXXXXXXXX---------------AAAATAAACAAATAGGG ----

    how can I decide which one is for align score 154 from the output?

    thanks

    Jian

  • #2
    The aligner will give you the best location(s) for the short read but in terms of deciding which one is the 5' or 3' miRNA this is not an alignment tool's decision.

    Working with pileups of all your reads mapped to the genome and looking at relative abundance of 5' and 3' read pileups will give you some indication of which is the mature small RNA.

    Comment


    • #3
      thanks zee,

      I did not want to know which one is 5'. I want to know the alignment score is from which part. i.e. forward or backward.

      for example in my previous example,
      the read is mapped to between xxxxxxxxxx and yyyyyyy.
      XXXXXXXXXXXXX--------AAAATAAACAAATAGGG---------YYYYYYYYYYYY

      the short sequence "AAAATAAACAAATAGGG" may complementary binding to XXXXXXXXX or YYYYYYYYYYYY. I want to know the aligment score 154 is from which one, xxxxxxxxxx or yyyyyyyyy.

      thanks
      jian

      Comment


      • #4
        Hi Jian,

        The score is from lower of the two possibilities but your right we don't indicate which one it is. The original idea was just to help locate which alignment was the precursor but not the orientation of the precursor. I can easily add the second location using field normally used for mate pair location in paired end processing.

        I'll add it to the next release.

        Colin

        Comment


        • #5
          Novoalign V2.07.03 is now available on www.novocraft.com.

          Changes include reporting the location of the hair pin alignment (i.e. the xxxxxxxx or yyyyyy as requested by jay2008)

          Comment

          Latest Articles

          Collapse

          • 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...
            Today, 06:43 AM
          • seqadmin
            Best Practices for Single-Cell Sequencing Analysis
            by seqadmin



            While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
            06-06-2024, 07:15 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 06-21-2024, 07:49 AM
          0 responses
          15 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-20-2024, 07:23 AM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-17-2024, 06:54 AM
          0 responses
          18 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-14-2024, 07:24 AM
          0 responses
          28 views
          0 likes
          Last Post seqadmin  
          Working...
          X