Hello Bert, One of our developers had these comments regarding your question:
If you want extra fields, it would be most efficient to just download the database table dump file, and use the cut program to extract the desired columns. The genomicSuperDups table is BED6, with an extra bin column and extra fields after BED6. BED with no extra fields doesn't have a way to represent the location of the duplicate sequence (otherChrom, otherStart, otherEnd). The Table Browser's BED and GTF output formats lose extra information from the tables, unfortunately. The Table Browser's selected fields output can keep the extra fields, but again, if you are going to do this often, might as well automate the downloading and field extraction instead of clicking all those field checkboxes in the Table Browser. As to whether Ensembl can make use of those extra fields in an uploaded track - that may require special software on their end. Hopefully this answered your question and if not please feel free to contact us again on the mailing list at [email protected]. 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
