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  • Bfast alignment



    I used Bfast to align my Chip-Seq data. Unfortunately the percentage of reads got aligned is very less.
    I used the default parameters to run 'matches' and 'local align'

    This is the log information:

    Performing alignment...
    Reads processed: 12000000
    Alignment complete.
    Performed 859254 local alignments.
    Outputted alignments for 112106 reads.
    Outputted 11887894 reads for which there were no alignments.
    Outputting complete.
    *********************************************************

    Please let me know.. why I get such a low percentage of aligned read in Bfast?

    Also i used Bowtie to align the same data, I got very different result:

    # reads processed: 12000000
    # reads with at least one reported alignment: 11220913 (93.51%)
    # reads that failed to align: 779087 (6.49%)
    Reported 11220913 alignments to 1 output stream(s)

    Thanks,
    Madhu
    Madhu

  • #2
    Is this SOLiD or Illumina data? Can you show us the commands you used, as well as the BFAST version #?

    Comment


    • #3
      This is Illumina data.
      I used ./bfast localalign -f ../../genomes/mm9_genome.fa -m $list\_matches.bmf -u -t > $list\_bfast.aligned.file.baf
      Madhu

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      • #4
        Remove the "-u" option.

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