Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • no. of alignments in bowtie2

    does bowtie2 have a default for number of alignments (-k parameter)?

    if so what is it? if not, how many alignments does it search for if i don't specify any k.

    my problem is basically that I'm aligning my reads through a database and there is a significant portion which is not aligned although it should be.
    Thanks for all help!

  • #2
    The default settings for bowtie2 (bowtie2 --help) are:
    Code:
    Reporting:
      (default)          look for multiple alignments, report best, with MAPQ
    And the parameters that determine how thoroughly it searches are:

    Code:
     Effort:
      -D <int>           give up extending after <int> failed extends in a row (15)
      -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)
    Unfortunately, that doesn't give the maximum attempted locations, merely the maximums for badly chosen seeds. I suspect it depends on how many close hits there actually are.

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      Non-Coding RNA Research and Technologies
      by seqadmin




      Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

      Nobel Prize for MicroRNA Discovery
      This week,...
      10-07-2024, 08:07 AM

    ad_right_rmr

    Collapse

    News

    Collapse

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