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  • Tabix on bed file

    Hello,

    I'm trying to use tabix on a bed file and it seems that tabix is unable to parse my file.
    Here is my file :

    Code:
    chr7    1000    5000    name1   1   +
    chr7    15000   25000   name3   4   +
    chr7    35000   75000   name4   8   +
    chr7    57373   987412  name5   16  -
    my commands are :
    $ bgzip example_sort.bed
    $ tabix -p bed example_sort.bed.gz

    and the outputs are :
    Code:
    [E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used?
    The offending line was: "chr7    1000    5000    name1   1   +"
    [E::get_intv] failed to parse TBX_GENERIC, was wrong -p [type] used?
    The offending line was: "chr7    15000   25000   name3   4   +"
    [E::hts_idx_push] Unsorted positions on sequence #4653157: 1 followed by 0
    tbx_index_build failed: example_sort.bed.gz

    Any ideas would be appreciated!
    Thanks

    Aubin

  • #2
    OK it works now, the problem was the automatic change of tabulations with 4 spaces with my f** text editor

    Comment

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