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  • - N options with maq 0.7.1

    why -N option is not working? I am not able to print mismatch positions?

    Anyone has used - N options with maq 0.7.1? Please clarify whether this option is available. It always prints 0 at the last column of mapview results in text format. Thanks.

    When I execute ./maq map, I get the options as below:

    Usage: maq map [options] <out.map> <chr.bfa> <reads_1.bfq> [reads_2.bfq]
    Options: -1 INT length of the first read (<=127) [0]
    -2 INT length of the second read (<=127) [0]
    -m FLOAT rate of difference between reads and references [0.001]
    -e INT maximum allowed sum of qualities of mismatches [70]
    -d FILE adapter sequence file [null]
    -a INT max distance between two paired reads [250]
    -A INT max distance between two RF paired reads [0]
    -n INT number of mismatches in the first 24bp [2]
    -M c|g methylation alignment mode [null]
    -u FILE dump unmapped and poorly aligned reads to FILE [null]
    -H FILE dump multiple/all 01-mismatch hits to FILE [null]
    -C INT max number of hits to output. >512 for all 01 hits. [250]
    -s INT seed for random number generator [random]
    -W disable Smith-Waterman alignment
    -t trim all reads (usually not recommended)
    -c match in the colorspace
    Anyone knows that whether maq 0.7.1 has -N options working or do I have start using maq 0.6.8?

    Thanks.

  • #2
    I wonder how -e will influence the results? How much should I set for the 100pe reads.

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