Add gene annotations to CHANGE-seq off-targets table

Summary

Annotate off-targets using gencode gtf file (e.g., exon, intron, TSS, intergenic).

An example output shown below, two addtional columns are added to the original CHANGE-seq table; they are genomic features and gene name (if off-targets occur in exon, intro, TSS, or TTS.)

../../_images/change_seq_output.png

Usage

Step 1

hpcf_interactive -q standard -R "rusage[mem=16000]"

Step 2

module purge

module load python/2.7.13 homer/4.9.1

Step 3

To see the help message:

python /home/yli11/HemTools/bin/add_gene_annotation.py -h

To run an example, takes about 5 min:

python /home/yli11/HemTools/bin/add_gene_annotation.py -f CRL688_CCR5_site_4_identified_matched.txt

output file: CRL688_CCR5_site_4_identified_matched.annot.txt

code @ github.