Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Anyone using Bowtie2 for ChIP-Seq?

    Hi,

    Is anyone using Bowtie2 for ChIP-Seq?
    Everyone seems to be using Bowtie 1.
    I have no one with whom to discuss the best settings for ChIP-Seq with Bowtie2.

    I just align the reads with the default settings for Bowtie2.
    I've already completed several analyses, and the results seem correct, but I have nagging doubts that I'm not doing it properly.

    For example, those using Bowtie1 often put the parameter --best.
    Should I be filtering my alignments after running Bowtie2 to keep only best alignments?

    Any feedback is appreciated, even if it is to tell me that I should just be using Bowtie1 like everyone else.

    Thank you,

    Alexis

  • #2
    Hi Alexis,

    Typically, we choose whether to use bowtie 1 or 2 depending on the read length of the library. As ChIP-Seq libraries are often sequenced using relatively short reads (around 50bp or less), bowtie 1 is probably more suitable for alignment.

    The --best parameter isn't really applicable in bowtie2 because it handles alignments differently to bowtie1. The defaults in bowtie2 are pretty sensible, so if your results look correct then you're probably fine.

    Phil

    Comment


    • #3
      Great.
      Thanks for your answer tallphil.
      I feel better that I'm not delivering results that are completely false.

      I've been using bowtie2 simply because 2 sounds better, and bowtie2 can handle compressed FASTQ files directly.

      My reads are paired end 50 bases. The documentation on the bowtie2 website is a bit ambiguous since they recommend bowtie2 for reads longer than 50 bases, and say that bowtie1 may or may not be better for reads shorter than 50 bases. I may be a bit picky but they don't say anything about reads exactly 50 bases long.

      I should probably switch to bowtie1 for my 50 bases long paired end ChIP-Seq, since it seems to be much more widely used that bowtie2.

      It would be interesting to do a comparison of the 2 programs on 50 bases paired end ChIP-Seq, but since the programs are constantly being updated the comparison would have to be repeated for each update.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Recent Advances in Sequencing Technologies
        by seqadmin







        Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

        Long-Read Sequencing
        Long-read sequencing has...
        Yesterday, 01:49 PM
      • 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

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 09:29 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 09:06 AM
      0 responses
      33 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 08:03 AM
      0 responses
      22 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 11-22-2024, 07:36 AM
      0 responses
      65 views
      0 likes
      Last Post seqadmin  
      Working...
      X