Peak Annotation using GREAT

Step 1

hpcf_interactive -q standard -R "rusage[mem=2000]"

Step 2

module purge

module load conda3

source activate /home/yli11/.conda/envs/share_url

Step 3

pyGREAT.py -f [your narrowpeak or bed file] --email

Note

Click on the URL in the email. You may need to wait for 1 minute to see the result.

Tip

The default genome is hg19. You can change it using -g option.

usage: pyGREAT.py [-h] [--email] -f INPUT [-g GENOME]

optional arguments:
  -h, --help            show this help message and exit
  --email               send email (default: False)
  -f INPUT, --input INPUT
                        input bed file (default: None)
  -g GENOME, --genome GENOME
                        No hg38. Please choose from hg19, mm9 or mm10.
                        (default: hg19)

code @ github.