2. CpG_anno_position.py

2.1. Description

This program adds annotation information to each CpG based on its genomic position.

2.2. Notes

Input CpG (-i) and annotation (-a) BED files must have at least three columns, and must based on the same genome assembly version
If multiple regions from the annotation BED file are overlapped with the same CpG site, their names will be concatenated together.
Since the input (-i) is a regular BED foramt file, this module can be uesd to annotate any genomic regions of interest.

2.3. Pre-computed datasets

hg19_ENCODE_338TF_130Cell_E3.bed.gz (File size = 108.2 MB): Transcription factor (TF) binding sites identified from ChIP-seq experiments performed by the ENCODE project. Peaks from 1264 experiments representing 338 transcription factors in 130 cell types are combined (N = 10,560,472). BED format file was downloaded from the UCSC Tabel Browser.
hg19_ENCODE_DNaseI_125Cells_V3.bed.gz (File size = 24.3 MB): DNase I hypersensitivity sites identified from ENCODE DNase-seq experiments. Peaks from 125 cell types are combined (N = 1,867,665). BED format file was downloaded from the UCSC Tabel Browser.
hg19_ENCODE_chromHMM_states_9Cells.merge.bed.gz (File size = 32.7 MB): Chromatin State Segmentation by chromHMM from ENCODE. Chromatin states across 9 cell types (GM12878, H1-hESC, K562, HepG2, HUVEC, HMEC, HSMM, NHEK, NHLF) were learned by integrating 9 factors (CTCF, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H4K20me1 ) plus input. A total of 15 states were identified, include: State-1 (Active Promoter), state-2 (Weak Promoter), state-3 (Inactive/poised Promoter), state-4 and 5 (Strong enhancer), state-6 and 7 (Weak/poised enhancer), state-8 (insulator), state-9 (Transcriptional transition), state-10 (Transcriptional elongation), state-11 (Weak transcribed), state-12 (Polycomb-repressed), state-13 (Heterochromatin or low signal), state-14 and 15 (Repetitive/Copy Number Variation). The Original chromatin state BED file was downloaded from the UCSC Tabel Browser.
hg19_FANTOM_enhancers_phase_1_and_2.bed.gz: PHANTOM5 human permissive enhancers downloaded from here.
hg19_ENCODE_H3K4me1_11_cellLines_ChIP.bed.gz (File size = 12.2 MB): H3K4me1 (marker of active and primed enhancer) peaks identified from ENCODE histone ChIP-seq experiments. Peaks from 11 cell types (GM12878, H1-hESC, HMEC, HSMM, HUVEC, HeLaS3, HepG2, K562, Monocytes-CD14+_RO01746, NHEK, NHLF) are combined (N = 1,435,550)
hg19_ENCODE_H3K4me3_11_cellLines_ChIP.bed.gz (File size = 4.5 MB): H3K4me3 (marker of promoter) peaks identified from ENCODE histone ChIP-seq experiments. Peaks from 11 cell types (GM12878, H1-hESC, HMEC, HSMM, HUVEC, HeLaS3, HepG2, K562, Monocytes-CD14+_RO01746, NHEK, NHLF) are combined (N = 525,824)
hg19_ENCODE_H3K27ac_11_cellLines_ChIP.bed.gz (File size = 5.7 MB): H3K27ac (marker of active enhancer) peaks identified from ENCODE histone ChIP-seq experiments. Peaks from 11 cell types (GM12878, H1-hESC, HMEC, HSMM, HUVEC, HeLaS3, HepG2, K562, Monocytes-CD14+_RO01746, NHEK, NHLF) are combined (N = 665,650)

These BED files were lifted over to hg38/GRCh38 using CrossMap. The hg38-based annotation files are available from here

2.4. Options

--version

show program’s version number and exit

-h, --help

show this help message and exit

-i INPUT_FILE, --input_file=INPUT_FILE

Input CpG file in BED3+ format.

-a ANNO_FILE, --annotation=ANNO_FILE

Input annotation file in BED3+ format.

-w WINDOW_SIZE, --window=WINDOW_SIZE

Size of window centering on the middle-point of each genomic region defined in the annotation BED file (i.e., window_size*0.5 will be extended to up- and down-stream from the middle point of each genomic region). if –window = 0, do NOT place window. default=100

-o OUT_FILE, --output=OUT_FILE

The prefix of the output file.

-l, --header

If True, the first row of input CpG file is header. default=False

2.5. Input files (examples)

2.6. Command

$CpG_anno_position.py  -l -a hg19_ENCODE_338TF_130Cell_E3.bed.gz -i test_01.hg19.bed6 -o output

2.7. Output files

output.anno.txt

$ head -5 output.anno.txt
#Chrom Start   End     Name    Beta    Strand  hg19_ENCODE_338TF_130Cell_E3.bed
chr1   10847   10848   cg26928153      0.8965  +       N/A
chr1   10849   10850   cg16269199      0.7915  +       N/A
chr1   15864   15865   cg13869341      0.9325  +       N/A
chr1   534241  534242  cg24669183      0.7941  +       FOXA2,MNT