I want to extract TSS ids with correspodning location for Hg19. Once
extract such TSS coordinates I want to have there annotation either
enetrz gene id or some other unique Ids. I am sure Galaxy can do this,
dont know where to start, or which workflow to use. Can some one
dircet me to right dircetion. Appreciate your help.
One direct method is to import data using "Get Data -> BioMart".
Choose "ENSEMBL GENES 62", then "Homo sapiens genes (GRCh37.p3)". In
left side bar, click on "Attributes". In the resulting form, select
"Structures", then open GENE and check "Transcript Start" and
"Associated Gene Name/DB" (plus whatever else you wish to include).
selection is complete, click on "Results" in the top menu bar, then in
the next form choose "Export all results to Galaxy" and GO.
There are other gene track sources (UCSC, etc.) that you may wish to
explore. If you need more help, please let us know,