Hello again Bert,
Our developers pointed out that as an alternative to the method from our
previous reply you could also use the following mysql statements.
( mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A \
-e "select chrom,chromStart,chromEnd,name from genomicSuperDups;" hg19;
mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A \
-e "select otherChrom,otherStart,otherEnd,name from
genomicSuperDups;" hg19) | sort -u | sort -k1,1 -k2,2n
Note that this method returns any {otherChrom, otherStart, otherEnd}
sets that would otherwise be lost (in the other method) for lack of a
corresponding {chrom, chromStart, chromEnd}.
You may also be interested to know that you could use our remote mysql
access to get any/all fields of genomicSuperDups in case you do want to
keep the pairings of {chrom, ...} with {otherChrom, ...}.
Best regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
On 5/16/12 2:15 AM, Bert Overduin wrote:
> Hello,
>
> I am trying to create a GTF or BED file for the Segmental Duplications
> using the Table browser with the goal to upload or attach the resulting
> file to Ensembl.
> Both the BED and GTF file generated by the Table browser do contain the
> position of the Segmentale Duplications, so these are shown correctly in
> Ensembl when uploaded, but the coordinates of the other position in the
> genome where the duplication can be found (which is crucial information)
> is missing from both the BED and the GTF file. Maybe I am doing something
> wrong though. Please advise.
>
> Cheers,
> Bert
>
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