Tabix on bed file can't parse
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 :
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
1 answer
Make sure that the columns are separated by a tab and not by whitespaces. (This is what Pierre is trying to check ;) )
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what are the outputs of
and
That last error seems to suggest an unsorted file (although the name would suggest its sorted). What command did you use to sort the file?
It's unclear what is wrong with the first two errors, they look like perfectly good bed lines, but I can think of two possiblities:
Can you post the output of
OK it works now, the problem was the automatic change of tabulations with 4 spaces with my f** text editor
Thanks for the help!
nibua