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  • help using tabix

    Dear All

    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.

    I would like to use the intervals generated by tabix and store them in a database for querying my sequence data from a RDMS. Is it possible to use tabix to
    a) generate the bin that a sequence resides in
    b) generate the bins that would need to be queried to get all feature within (or overlapping) a sequence region

    Is tabix suitable for this purpose? Being as I can't view the index file at present its difficult to answer myself. I suspect the index file will only contain the bin a sequence resides in and will not be suitable for finding the bins to query for a sequence range. If tabix, is there anything else you could recommend?

    thank you for your help

    Also, what the interval sizes used by tabix? I could not find details of this. Can you control them?

  • #2
    Tabix allows you to access a file by quering for (for example) a chromosome and position and retrieve all the lines of that file that match your query.

    Problems arise when you need to do thousands of lookups. Tabix can take hours to do, say, 100k lookups into DBSNP data. I wrote a Perl/C++ (Text::Tidx) alternative to tabix for annotating Exomes, using DBSNP or 1K genomes data. It uses a lot of RAM, but is much faster than tabix for that stuff.

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