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  • Reference genome for MAQ - split reference genome by chromosome or not?

    Hello!
    I am a beginner!
    I am trying MAQ..
    My question is about the reference genome! I downloaded the mm9 genome from UCSC, and it comes as separated chr*.fa files (one fasta per chromosome)

    However, the MAQ command to do the alignments points to a single file as the reference genome:

    maq match output.map genome.bfa myreads.bfq

    I converted all my chr.fasta files to bfa files using maq "fasta2bfa".
    Now, I don't know if i am supposed to run the MAQ for each single chromosome individually or if I should have the complete genome in one-single-bfa-file.

    Any of these is a challenge.
    If we the alignment is to run chromosome by chromosome then there should be a way to merge the output files (I think...!?).
    One the other hand, if the genome is supposed to be in just one-file, how do I do that?

    Any thoughts?
    THanks!!
    ines

  • #2
    here is a similar discussion => don't split by chromosome
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc
    --
    bioinfosm

    Comment


    • #3
      Good to know!

      I can't find the complete genome in the UCSC database.
      Should I do it myself? merge my chromosome.fa files into one-big file looking like this:

      >chr1
      AACTGTGCACTGTGACAC...
      GTACGCACGTGCGTGCAC...
      >chr2
      ACATTGCCAACACTGTCA...
      ACACGTGCGTGCACACGT...
      >chr xyz

      I don't know if this is the right format...

      Comment


      • #4
        just a quick reply to myself:
        Yes, that's the right format!

        Comment


        • #5
          Yes, sometimes eland gives issues with fasta headers, it creates extra columns in the export or eland_extended output. So I also prefer to keep the fasta reference sequence headers small
          --
          bioinfosm

          Comment

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