Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Disregard (not sure how to delete post)

    Nevermind. When I ran the alignments in Bowtie I forgot to remove the "-S" parameter.

    *****************

    I never really noticed this before, but Bowtie doesn't show - or + strand assignment. Instead it seems to give a code for what strand it aligns to in the second column of the output (SAM or Bowtie format).

    The Bowtie manual says that the flag '16' represents the alignment to the reverse (-) reference strand. In my data I see '16', '0', '4' as alignment flags in the second column, '4' representing no alignment.

    A flag '0' represents alignment to the forward (+) strand? Is that correct?

    Just want to verify that.


    Thanks.
    Last edited by DrD2009; 08-07-2010, 02:08 PM.

  • #2
    You cant delete your own posts, but I will delete this one if you want. In the future, the community would benefit from leaving your thread/question intact, as someone else could certainly make the same mistake.

    Comment


    • #3
      Ah. You can keep it up if you think it will be beneficial to others.

      Comment


      • #4
        Cool. Thanks for putting the title back!

        Comment


        • #5
          Not a problem.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM
          • seqadmin
            Techniques and Challenges in Conservation Genomics
            by seqadmin



            The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

            Avian Conservation
            Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
            03-08-2024, 10:41 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 06:37 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          9 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          50 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          67 views
          0 likes
          Last Post seqadmin  
          Working...
          X