= Data Sources =

[[TOC()]]

For this practical we will use the [http://www.ensembl.org Ensembl Genome Browser].

 * Create an account on [http://www.ensembl.org www.ensembl.org] I you don't already have one, 
   so you can create custom tracks and save them for future visits.
 * Login on [http://www.ensembl.org www.ensembl.org]

== Verify exome capturing kit annotation ==

If you are looking for genetic variation in human protein coding genes, sequencing the whole genome is not economical as the human exome as only ~ 2% of the genome. To enrich the NGS analysis you can order capturing kits for your genes of interest. The latest version of the most popular exome capturing kit is the !SureSelect All Exon capturing kit version 5 from Agilent. Will your genes of interested be covered completely and captured well with this kit? In other words what was the manufacturer's definition of ''"whole Exome"'' at the time of the design of this kit?

To check this we will:
 * upload the *.bed file describing the regions for which probes were designed in the Ensembl Genome browser.
 * Please note that this info is for build GRCh37 of the human genome. So locate the last Ensembl version GRCh37.
 * Search for your gene of interest
 * Switch to the second tab in Ensembl for the ''location view''
 * Click the ''Configure this page'' button
 * In the popup window select the 4th tab ''Personal Data''
 * Go to ''Custom data'' -> ''Add your data'' in the column on the left and upload the [[attachment:AllExonV5.bed.gz|*.bed file for the SureSelect All Exon V5 kit]].
 * Click the checkmark at the top-right corner of the popup window to close it and wait for the display to update.
 * Optionally click ''Configure this page'' again and enable/disable other annotation tracks
 * Inspect your gene of interest: does the capturing kit capture all exons completely?

== Verify custom capturing kit annotation==

For a more targeted approach we designed a capturing kit for all genes from the Clinical Genomics Database (CGD). Upload the [[attachment:CGD_2014-03-12.bed.gz|*.bed file for this capturing kit]] too and check if this more recent kit is better for your genes of interest. If your gene of interest was not part of the CGD, you can search for example for any of these genes: DNMT1, ATXN8, ATXN8OS or DSG1.

== BioMart ==