Question: Help Using Tabix
1
gravatar for Pi
3.0 years ago by
Pi450
Pi450 wrote:

Greetings

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

ADD COMMENTlink modified 3.0 years ago by Istvan Albert ♦♦ 39k • written 3.0 years ago by Pi450
5
gravatar for Istvan Albert
3.0 years ago by
Istvan Albert ♦♦ 39k
University Park, USA
Istvan Albert ♦♦ 39k wrote:

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.

ADD COMMENTlink written 3.0 years ago by Istvan Albert ♦♦ 39k
1

It is best if we stick to the question that you ask here, it seems that you are merging two unrelated concepts. tabix is a command line tool that allows you to perform a interval query outside of a database - it has nothing to do with and cannot be combined with database binning schemes.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 39k

Thanks for your reply. I appreciate the point you are making and I did make a comment on the previous question to address that point but perhaps you did not see it? Would you be so kind as to revisit the previous question? Also it would really help if you could you comment on my point about interval sizes and colocated snps. Thank-you for your time

ADD REPLYlink written 3.0 years ago by Pi450

ok - tabix is not suitable for my needs. shall i close the question?

ADD REPLYlink written 3.0 years ago by Pi450

i have also added an edit to my previous question about interval sizes. I would really appreciate it if you could revisit the question and address that point

ADD REPLYlink written 3.0 years ago by Pi450
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