Getting ready

Our simple example will use data from the region where the LCT gene is located in the human genome. The LCT gene codifies lactase, an enzyme involved in the digestion of lactose.

We will take this information from Ensembl. Go to http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000115850 and choose Export data. The Output format should be BED Format. Gene information should be selected (you can choose more if you want). For convenience, a downloaded file is available in the Chapter02 directory, called LCT.bed.

The Notebook for this code is called Chapter02/Processing_BED_with_HTSeq.ipynb.

Take a look at the file before we start. An example of a few lines of this file is as follows:

track name=gene description="Gene information"
 2       135836529       135837180       ENSE00002202258 0       -
 2       135833110       135833190       ENSE00001660765 0       -
 2       135789570       135789798       NM_002299.2.16  0       -
 2       135787844       135788544       NM_002299.2.17  0       -
 2       135836529       135837169       CCDS2178.117    0       -
 2       135833110       135833190       CCDS2178.116    0       -

The fourth column is the feature name. This will vary widely from file to file, and you will have to check it each and every time. However, in our case, it seems apparent that we have Ensembl Exons (ENSE...), Genbank records (NM_...), and coding region information (CCDS) from the CCDS database (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi).