Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Paired-end reads mapped 50% while each pair reads mapped 80%

    Hi all,

    I am new to the RNA seq world. I have processed bunch of illumina paired end reads. The reported alignment is only 49%.. When I use bowtie to map each pair of the paired-end reads, I got 80% of the reads mapped.

    bowtie -n 3 -p 10 --best -e 200 --trim5 15 --trim3 25 --sam BowtieIndexes/mm9 -1 Raw_files/sample-1_export.fq -2 sample-2_export.fq sample.sam


    # reads processed: 21482797
    # reads with at least one reported alignment: 10637665 (49.52%)
    # reads that failed to align: 10845132 (50.48%)
    Reported 10637665 paired-end alignments to 1 output stream(s)


    I was wondering if this is normal. Here's the command and output. Thanks.

    P.S.: This is my 3rd post on this forum. I posted a similar question in my 2nd post. However, I can no longer reply that post.


    ----- I couldn't post a reply, so here it goes ----

    Isn't it that tophat also uses bowtie to align reads?
    Last edited by zack80.liu; 03-02-2011, 03:48 PM.

  • #2
    You shouldn't be using bowtie for RNA-seq (especially with PE reads) - try tophat or another one of the splicing-aware aligners

    Comment


    • #3
      Isn't tophat also use bowtie to do the alignment?

      Comment


      • #4
        Dear Zack,

        The most likely explanation would indeed be that a sizeable fraction of you library fragments are spanning a splice junction. In these cases many fragments in your library are longer than the allowed Bowtie default fragment size of 250bp (These parameters can be adjusted with
        -I/--minins <int> Default: 0.
        -X/--maxins <int> Default: 250)

        Using TopHat or any other splice junction aware aligner should indeed fix your problems.

        Comment

        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, 07-16-2024, 05:49 AM
        0 responses
        23 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-15-2024, 06:53 AM
        0 responses
        31 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-10-2024, 07:30 AM
        0 responses
        40 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-03-2024, 09:45 AM
        0 responses
        205 views
        0 likes
        Last Post seqadmin  
        Working...
        X