Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • strand bias tools

    Does anyone know any tools for mapping regions of strand bias?

    I want to simply create a bed file of regions where there is strand bias above or below a certain threshold.

  • #2
    Hi,

    What are you referring to by strand bias? Is this same as the mapping orientation? Do you wish to constrain reads so that they map to one strand and not the other?

    Comment


    • #3
      Originally posted by Apexy View Post
      Hi,

      What are you referring to by strand bias? Is this same as the mapping orientation? Do you wish to constrain reads so that they map to one strand and not the other?
      Yes I am referring to strand orientation. Due to the assay, there is a disproportionate number of reads (only in particular regions) mapped in a single direction versus the other direction. This also affects the reads with called variants. There is bias towards a given strand in some cases. As a result some variants that are known variants are not called. I would like to map these regions so that I know how many potential regions/bases this affects.

      Comment


      • #4
        Hi Mutagenic,
        I am aware that in bowtie, there is an option (--nofw/--norc) which can allows you do this type of thing but I have not used it. It is possible that other alignment tools might have a similar option.
        Hope this helps!

        Comment


        • #5
          did you find a tool for strand bias calculatio ?

          Originally posted by Mutagenic View Post
          Yes I am referring to strand orientation. Due to the assay, there is a disproportionate number of reads (only in particular regions) mapped in a single direction versus the other direction. This also affects the reads with called variants. There is bias towards a given strand in some cases. As a result some variants that are known variants are not called. I would like to map these regions so that I know how many potential regions/bases this affects.
          Hi,
          I'm also trying to find a tool to obtain strand bias regions. Dealing with Sam file is quite tricky. Did you find any tool or perl/python library to do the job?
          thanks very much in advance.
          S.

          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,...
            11-06-2024, 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, 11-08-2024, 11:09 AM
          0 responses
          224 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 11-08-2024, 06:13 AM
          0 responses
          166 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 11-01-2024, 06:09 AM
          0 responses
          80 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 10-30-2024, 05:31 AM
          0 responses
          27 views
          0 likes
          Last Post seqadmin  
          Working...
          X