Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Filtering out transcriptome data

    Hi,
    I have RNA-Seq reads of mutant plant which has few insertions (unknown sequence) in comparison to wild reference genome. I want to filter out all reads which are the same as in reference so I can get only those insertion sequences. Should I map my reads straight to reference to filter it out or try to do de novo assembly and then map contigs to reference genome? What do you suggest?

  • #2
    A quick solution would be to use bowtie with the option --un; which writes unmapped reads to a file and then work with that.

    Comment


    • #3
      Thanks cascoamarillo, I will proceed as you suggested. But using bowtie2 will remove also reads which are located at exons boundaries so that I will get those files in unmapped reads, am I correct?
      Last edited by Ahaswer; 03-23-2015, 08:44 AM.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Genetic Variation in Immunogenetics and Antibody Diversity
        by seqadmin



        The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
        Yesterday, 07:24 PM
      • seqadmin
        Choosing Between NGS and qPCR
        by seqadmin



        Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
        10-18-2024, 07:11 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 11-01-2024, 06:09 AM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-30-2024, 05:31 AM
      0 responses
      21 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-24-2024, 06:58 AM
      0 responses
      25 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-23-2024, 08:43 AM
      0 responses
      56 views
      0 likes
      Last Post seqadmin  
      Working...
      X