How do you view the tbi file generated by tabix? I am using tabix v0.2.5 to index a local BED file of gene positions. The tbi index file is bgzipped. I can read the bgzipped BED file using the commands you would expect (e.g. zless)
I would like to use the intervals generated by tabix and store them in a database for querying my sequence data from a RDMS. I need to:
a) generate the bin that a sequence resides in
b) generate the bins that would need to be queried to get all features within (or overlapping) a sequence region
The need for this was discussed in this question
Being as I can't view the index file I'm a bit stuck at proceeding. However I am concerned that tabix index file will only contain the bin a sequence resides and that the software tool (from reading the docs) doesn't provide a means of obtaining the bins to query for a sequence feature
thank you for your help
I think you are misunderstanding what tabix does. It is a tool that allows you to perform fast interval queries based on tab delimited interval file, like so:
tabix sorted.gff.gz chr1:10,000,000-20,000,000;
This above queries the sorted.gff.gz file for the positions listed on the right.
The index that it creates is based on your gff file. But this index is only used by tabix to allow you to perform fast queries, typically there is no point in trying to use it yourself. As for the previous question - the advice was to perform the query with tabix then based on its output update the database.