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Old 06-26-2019, 12:06 AM   #1
bluesmartini
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Location: Montpellier

Join Date: Jun 2014
Posts: 4
Default 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
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Old 06-27-2019, 12:39 AM   #2
bluesmartini
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Location: Montpellier

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Posts: 4
Default

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