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  • tmap mapall usage

    Hello everybody,

    I camming from "bowtie world" and illumina sequencing...

    but now I'm received a ion proton library and I want mapp that reads in a reference genome... I've found that TMAP tool is a better tool than bowtie and soap for ion proton reads...

    I've no success in using the mapall algorithm

    when I trying a error happens in "tmap_map_opt_check"

    probably, there are some options that weren't used... but which one??
    the manual didn't show any usefull information about that...

    does anybody have a template for tmap mapall default commands?

    like:
    tmap mapall -f reference.fas -r lib.fastq -s out.sam etc.....


    thanks

  • #2
    Originally posted by guil View Post
    Hello everybody,

    I camming from "bowtie world" and illumina sequencing...

    but now I'm received a ion proton library and I want mapp that reads in a reference genome... I've found that TMAP tool is a better tool than bowtie and soap for ion proton reads...

    I've no success in using the mapall algorithm

    when I trying a error happens in "tmap_map_opt_check"

    probably, there are some options that weren't used... but which one??
    the manual didn't show any usefull information about that...

    does anybody have a template for tmap mapall default commands?

    like:
    tmap mapall -f reference.fas -r lib.fastq -s out.sam etc.....


    thanks
    The mapall command requires you to specify the mapping algorithms, so something like:
    tmap mapall -f reference.fas -r lib.fastq -s out.sam map1 map2 map3

    See: https://github.com/iontorrent/TMAP/b.../tmap-book.pdf

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