Question: Tss List With Annotation For Hg19
gravatar for shamsher jagat
7.5 years ago by
United States
shamsher jagat590 wrote:
I want to extract TSS ids with correspodning location for Hg19. Once I extract such TSS coordinates I want to have there annotation either with enetrz gene id or some other unique Ids. I am sure Galaxy can do this, But I dont know where to start, or which workflow to use. Can some one please dircet me to right dircetion. Appreciate your help.
galaxy • 1.8k views
ADD COMMENTlink modified 7.5 years ago by Jennifer Hillman Jackson25k • written 7.5 years ago by shamsher jagat590
gravatar for Jennifer Hillman Jackson
7.5 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello, One direct method is to import data using "Get Data -> BioMart". Choose "ENSEMBL GENES 62", then "Homo sapiens genes (GRCh37.p3)". In the 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). When 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, Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 7.5 years ago by Jennifer Hillman Jackson25k
Short update: I forgot to mention that you will probably want to include the chromosome and strand under the "GENE" options. Also, do not select "Associated Gene DB" during the export (just examine this at BioMart to note the source) as this will output some html content not allowed in a Galaxy history dataset. Hopefully this helps, Jen -- Jennifer Jackson
ADD REPLYlink written 7.5 years ago by Jennifer Hillman Jackson25k
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