Question: tabix a text file
1
gravatar for vigprasud
4.3 years ago by
vigprasud60
United States
vigprasud60 wrote:

Is there a way to tabix a text file and use it for quick retrieval of records?

I have these fields in a text file 

#CHR START STOP GENE

I would like to retrieve the records based on chr:start-pos. 

 

My sample file [sample.txt] has this data

chr1    11873   14361   A
chr1    14469   29370   B
chr1    34610   36081   C
chr1    69090   70008   D
chr1    134772  140566  E
chr1    323891  328581  F
chr1    367658  368597  G

 

I bgzipped it to get sample.txt.gz file

I tabixed with the following command 

 tabix -b 1 -e 3 -S 0 -0 sample.txt.gz and this is the error i encountered

[get_intv] the following line cannot be parsed and skipped: chr1        11873   14361   A
[ti_index_core] the indexes overlap or are out of bounds

Any ideas on how to tabix a text file??

 

text tabix • 2.5k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 4.3 years ago by vigprasud60
7
gravatar for Pierre Lindenbaum
4.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

 'start' is in column 2 , you used -b 1

you'd better use the predefined setting tabix -p bed

ADD COMMENTlink written 4.3 years ago by Pierre Lindenbaum121k
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