Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • A great tool to count multiple aligned reads.

    Dear members of seqanswers,

    Do you know a tool for counting multiple aligned reads?

    Currently I use the htseq-count tool, but it doesn't take into account this type of read.

    I know cufflinks allows this kind of thing, but I do not like this tool, because for me it is a "black box".

    There are some time ERANGE allowed to do this assigning multiple aligned reads in the proportion of single aligned reads in each respective region. I find it effective, unfortunately ERANGE is no longer maintained.

    I thank you in advance for your help.

    Best,
    a.kmg

  • #2
    The appropriate tool will depend on how you want the reads counted. featureCounts is one option, though obviously if you're counting over genes and using those integer counts to look at differential expression then this is a bad idea. Other options would be things like eXpress or any other tool meant to generate expected counts using a expectation maximization method. This will yield fractional counts, which is appropriate for multimapped reads.
    Last edited by dpryan; 01-27-2015, 02:08 AM.

    Comment


    • #3
      Thank you dpryan.

      I currently testing Rcount, a new tool where alignments of multireads are weighted based on the number of uniquely aligned reads in the neighborhood.

      And I tested featureCount, that actually allows me to treat multiple aligned reads, but the fact of counting the reads for each chromosomal locations on which it aligns leads to a biais, right?

      Comment


      • #4
        Originally posted by a.kmg View Post
        And I tested featureCount, that actually allows me to treat multiple aligned reads, but the fact of counting the reads for each chromosomal locations on which it aligns leads to a biais, right?
        Not really. The reads arose from the neighboring reads, so the counting would accurately represent the biological reality.

        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