Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie colorspace output has less NT than input reads

    Hi,

    I am using bowtie for colorspace alignment. My data are 35nt reads (36nt if the first T is included). In the bowtie default output file, the decoded sequence space reads has only 33 NT displayed.

    my command is:

    bowtie -t -q -p 7 -C -n 3 -a --best MyGenomeSeq MyInput.fastq > MyOutput.aln &

    Could anyone explain this?

    Thanks,
    Song Li

  • #2
    Hi SongLi,
    one of the options in bowtie is trimimng bases from:
    " -5/--trim5 <int>
    Trim <int> bases from high-quality (left) end of each read before alignment (default: 0).

    -3/--trim3 <int>
    Trim <int> bases from low-quality (right) end of each read before alignment (default: 0). "

    maybe you used it?

    Ilia

    Comment


    • #3
      Hi,

      Thank you for the reply. My command is included in my previous post. I did not use --trim unless it was default for colorspace alignment.

      Best,
      Song

      Originally posted by zhidkov.ilia View Post
      Hi SongLi,
      one of the options in bowtie is trimimng bases from:
      " -5/--trim5 <int>
      Trim <int> bases from high-quality (left) end of each read before alignment (default: 0).

      -3/--trim3 <int>
      Trim <int> bases from low-quality (right) end of each read before alignment (default: 0). "

      maybe you used it?

      Ilia

      Comment


      • #4
        --trim option suppose to be 0 by default...

        Comment


        • #5
          Ok, found this:


          think it has the answer you looked for

          PS
          Learned something new myself, thank you

          Comment


          • #6
            Thank you for pointing out this link.



            Originally posted by zhidkov.ilia View Post
            Ok, found this:


            think it has the answer you looked for

            PS
            Learned something new myself, thank you

            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
            221 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 11-08-2024, 06:13 AM
            0 responses
            163 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