Uploading ENCODE datasets

Though we found the SNP we were looking for, in reality you would not know if the phenotype-associated SNP was a coding or non-coding SNP. We will look at the non-coding SNPs as well here.

To bring in the ENCODE data we will use the Upload File tool in the section Get Data (red arrow). One way to import large datasets into Galaxy is from an URL. Copy and paste the URLs from below. These datasets are combined across labs and cell lines. One is DNase hypersensitive sites and the other is transcription factor occupied segments. Select the Genome hg19 and then click Execute (green arrow). This will load both datasets separately in the history. Once the datasets have loaded rename them to "ENCODE DHS" and "ENCODE TFos".

http://www.bx.psu.edu/miller_lab/docs/galaxy_phen_assoc/tutorial/dhsEncode2012.interval.gz
http://www.bx.psu.edu/miller_lab/docs/galaxy_phen_assoc/tutorial/tfosEncode2012.interval.gz