How to obtain updated (or versioned) refFlat files

[Owen Solberg]

Hello,

I've been using this refFlat file in my analysis:

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refFlat.txt.gz

The datestamp on this file says:  27-May-2018 09:35

... but the README viewable from the same directory states:

This directory contains a dump of the UCSC genome annotation database for the
    Dec. 2013 (GRCh38/hg38) assembly of the human genome
    (hg38, GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.2)) .

This accession number GCA_000001405.2 relates to GRCh38, patch 1.  Is the above mentioned refFlat.txt.gz file still based on patch 1?  Or is this file constantly updated?

Really, what I am trying to do is to obtain a refFlat file corresponding specifically to GRCh38 p11 (aka GenCode v27).   The following SQL command (querying UCSC's public hg38 database) seems to get me pretty close, but there  seem to be too many rows:

`select name2, name, chrom, strand, txStart, cdsStart, cdsEnd, exonCount, exonStarts, exonEnds from wgEncodeGencodeBasicV27`

Any help or advice is greatly appreciated.

Thanks

Owen

[Christopher Lee]

Hello Owen,

Thank you for your questions about refFlat.txt.gz and the MySQL server. The refFlat.txt.gz file on the downloads server is updated constantly and is based on the first version of the GRCh38 assembly only, no patches.

Additionally, the Gencode V27 track is based on GRCh38.p10:
https://www.gencodegenes.org/releases/27.html

Our Gencode track is based on the "PRI" version of the V27 release, corresponding to all chromosomes and scaffolds, but not including new patch sequences.

The MySQL query you shared will obtain GENCODE V27 annotations in the refFlat format, and this file should differ from the refFlat.txt.gz file because RefSeq and Gencode are different annotation sources.

If I have misunderstood your questions please let us know!

Thanks,

Christopher Lee
UCSC Genomics Institute

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