Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Comparing Merged Seqs to a Reference Seq

    Hello,

    I recently received paired-end reads from an amplicon library I sequenced with Illumina. I used BBMerge to merge the paired-ends and, now, I would like to compare my merged sequences to a reference. My goal is to analyze where the merged sequence may differ from the reference.

    I have tried to write a small Perl program, but I am continually running into problems. I study DNA repair and, essentially, I would like to compare my merged sequences to the reference so that I may better understand repair efficiency.

    Is anyone aware of any programs/scripts that could help me reach my goal of comparing my merges to a reference? They are about 200bp long. Thank you!

  • #2
    BBMap.sh (where you got BBMerge from) will do the comparisons/alignments.

    Added: Is your reference 200 bp long?

    Comment


    • #3
      Originally posted by GenoMax View Post
      BBMap.sh (where you got BBMerge from) will do the comparisons/alignments.

      Added: Is your reference 200 bp long?
      Yes, it is. Thank you, GenoMax! Will BBMap allow me to set any criteria for the alignment? For example, if I did not want any sequences that differ by more than 10% from my reference.

      Comment


      • #4
        Run bbmap.sh on its own to see all the command line options.

        Here are some relevant options

        Post-Filtering Parameters:

        idfilter=0 Independant of minid; sets exact minimum identity
        allowed for alignments to be printed. Range 0 to 1.
        subfilter=-1 Ban alignments with more than this many substitutions.
        insfilter=-1 Ban alignments with more than this many insertions.
        delfilter=-1 Ban alignments with more than this many deletions.
        indelfilter=-1 Ban alignments with more than this many indels.
        editfilter=-1 Ban alignments with more than this many edits.
        inslenfilter=-1 Ban alignments with an insertion longer than this.
        dellenfilter=-1 Ban alignments with a deletion longer than this.
        Last edited by GenoMax; 05-01-2015, 10:37 AM.

        Comment


        • #5
          You could also convert your reads to fasta format (use reformat.sh from BBMap) and then use blat for the alignments.

          Once you identify the reads that align I suppose you want to do a multiple sequence alignment?

          Comment

          Latest Articles

          Collapse

          • seqadmin
            The Impact of AI in Genomic Medicine
            by seqadmin



            Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
            02-26-2024, 02:07 PM
          • seqadmin
            Multiomics Techniques Advancing Disease Research
            by seqadmin


            New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

            A major leap in the field has
            ...
            02-08-2024, 06:33 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 02-28-2024, 06:12 AM
          0 responses
          25 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-23-2024, 04:11 PM
          0 responses
          72 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-21-2024, 08:52 AM
          0 responses
          81 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-20-2024, 08:57 AM
          0 responses
          69 views
          0 likes
          Last Post seqadmin  
          Working...
          X