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  • 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

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