Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • generating pileup of paired end fragments

    Dear all,
    i'm working with paired end rnaseq data. i wanted to generate a pileup with samtools mpileup but noticed that only the mapping reads get counted, and not the unmapped part between two mates, like so:

    ______READ1--------READ2________ <- mapping
    ______1 1 1 1 0 0 0 1 1 1 1________ <- pileup

    is generating pileups using the whole fragment (read + mate + part in between them) frowned upon for some reason? would it be correct to do it? if yes are there any tools?

    alternatively, is there a tool to merge mates and generate the complete fragment in a sam file?

    Thank you!
    Last edited by Slacanch; 01-20-2015, 08:42 AM.

  • #2
    What would a pileup of the uncovered region between mates even look like. They couldn't contribute any sequence, so what would you show for them? The only conceivable reason I could think of to do this is in peak calling for chip-seq or something like that, but then you don't care about the actual sequence so there'd be no point in going to full pileup route.

    Comment


    • #3
      well i don't really care about the sequence, it's for profile comparison.
      as long as the positions are right, i'm ok with it.

      maybe i shouldn't have called it pileup, but coverage. just a measure of how many reads overlap each position, in order to be able to compare profiles at certain loci (such as transcriptional readthrough for example).

      for future reference, i discovered a script that does more or less this in the "misc" folder of samtools. it's called interpolate_sam.pl.

      i'll check it more in detail and report back.

      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
      230 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