How to retrieve Annotation files from UCSC Table browser?

[alexg9010]

To perform annotation of your segmented methylomes or differentially methylated regions, PiGx-Bsseq uses two types of annotation files from UCSC: the CpG-Island annotation and the knownGene annotation.

To retrieve annotation files for humans( hg38) from UCSC Table Browser, follow these steps:

1. Go to the UCSC Table Browser website (https://genome.ucsc.edu/cgi-bin/hgTables).

2. Select the genome assembly you are working with from the drop-down menu.

3. Choose the group "Genes and Gene Prediction Tracks" and the latest "GENCODE" track with table "knownGene" for knownGene annotation,

or choose the group "Regulation" and the track "CpG Islands" for CpG-Island annotation.

4. Select the whole genome as the region of interest and choose "BED" as the output format and file type.

5. Click on the "get output" button to retrieve the annotation file.

6. Download the file and save it to your local directory for use with PiGx-Bsseq pipeline v0.1.9 or later.