Hello Andigoni, To confirm, the data is being extracted using "Get Data -> UCSC Main" using the Table browser for the hg16 reference genome? If so, I can let you know that the reference genome itself remains the same through time. However, annotation tracks may or may not be updated. Genbank track update frequencies are incremental daily additions and add/remove/change at full releases. From your numbers, it seem like the data is coming from RefSeq Genes. This track was last updated on "2012-04-07". This can be seem at UCSC when browsing the track's description page, the last line of the top section: "Data last updated:". The dates for the corresponding files on their downloads server will also reflect updates (server updated weekly). Unfortunately, there isn't a straightforward way to get back to your prior data unless you have it saved. If you have the exact date of your original data pull, you may be able to reconstruct part of it by mining GenBank directly, but this would be non-trivial and involve your own methods/tools outside of Galaxy. Hopefully this helps to explain the data content. If you have comments or questions about how tracks are processed at UCSC (including this question, they may have a creative solution), their team can be reached at: http://genome.ucsc.edu/contacts.html Going forward, please use our mailing list for questions. Thank you! Jen Galaxy team

---------- Forwarded message ---------- From: *andigoni* <andigoni@med.auth.gr <mailto:andigoni@med.auth.gr>> Date: Sun, Apr 8, 2012 at 7:06 PM Subject: Re: [galaxy-user] inconsistency with query results at different time periods

Dear Galaxy Gury,

I would like to ask you a simple question about the human genome assembly updates. Few months ago I extracted all the introns in bed format of chromosomes 6,20 and 22 using the hg16 assembly. The total number of records was 32.050.

Could you please explain why today the same query results in 32.837 introns? hg16 isn't a stable release? And how can I go back to the 32.050 introns in order to process them further?

Thank you very much in advance, Andigoni

Andigoni Malousi Post-doc in Bioinformatics Aristotle University of Thessaloniki