ICGC-ARGO Open-access regions definitions and bed files
- Genomic elements are defined according to the definitions in the table based on GENCODE annotations v38
- Open-access = CDS + Exon + UTR + Promoter + splice site + small ncRNA
- Control-access = complementary regions of Open-access upon whole genome
| Genomic Elements | Definition | Operation |
|---|---|---|
| Coding elements (CDS) | The set of coding bases collapsed across all coding transcripts with a given GENCODE gene ID. | feature_type=CDS |
| Exon | The set of exon bases collapsed across all transcripts with a given GENCODE gene ID. | feature_type=exon |
| 5'UTR (UTR5) | The set of 5’UTR bases collapsed across all coding transcripts with a given GENCODE gene ID. | feature_type=UTR |
| 3'UTR (UTR3) | The set of 3’UTR bases collapsed across all coding transcripts with a given GENCODE gene ID. | feature_type=UTR |
| Protein-coding promoter | Regions extending 200 bases in upstreaming direction from all protein-coding transcripts’ transcription start sites (5’ ends). Bases were collapsed across all coding transcripts with a given GENCODE gene ID. |
feature_type=transcript transcript_type=protein_coding locate the TSS for each transcript get the regions (-200, 0) upstreaming of TSS |
| Protein-coding splice site | Intronic regions extending 6 bases from donor splice sites and 20 bases from acceptor splice sites were collected for all coding transcripts Bases were collapsed across all coding transcripts with a given GENCODE gene ID. |
feature_type=transcript transcript_type=protein_coding locate all the introns and donor/acceptor splice sites for each transcript get the regions (-3,6) and (-20,3) around donor/acceptor splice sites |
| LncRNA | lncRNA transcripts were defined based on annotations from GENCODE. The elements were made by collapsing bases across transcripts with given GENCODE gene ID. |
feature_type=transcript transcript_type=lncRNA |
| LncRNA promoter | Regions extending 200 bases in upstreaming direction from all lncRNA transcripts’ transcription start sites (5’ ends). Bases were collapsed across all lncRNA transcripts with a given gene GENCODE ID. |
feature_type=transcript transcript_type=lncRNA locate the TSS for each transcript get the regions (-200,0) upstreaming of TSS |
| LncRNA splice site | Intronic regions extending six bases from donor splice sites and 20 bases from acceptor splice sites were collected for all lncRNA transcripts. Bases were collapsed across all lncRNA transcripts with a given gene GENCODE ID. |
feature_type=transcript transcript_type=lncRNA locate all the introns and donor/acceptor splice sites for each transcript get the regions (-3, 6) and (-20, 3) around donor/acceptor splice sites |
| smallRNA | smallRNA transcripts were defined based on GENCODE transcripts with biotype: ['Mt_rRNA', 'Mt_tRNA', 'miRNA', 'misc_RNA', 'rRNA', 'scRNA', 'snRNA', 'snoRNA', 'ribozyme', 'sRNA', 'scaRNA']. Bases were collapsed across all smallRNA transcripts with a given gene GENCODE ID. |
feature_type=transcript transcript_type in ['Mt_rRNA', 'Mt_tRNA', 'miRNA', 'misc_RNA', 'rRNA', 'scRNA', 'snRNA', 'snoRNA', 'ribozyme', 'sRNA', 'scaRNA'] |
| smallRNA promoter | Regions extending 200 bases in upstreaming direction from all smallRNA transcripts’ transcription start sites (5’ ends). Bases were collapsed across all smallRNA transcripts with a given gene GENCODE ID. |
feature_type=transcript transcript_type in ['Mt_rRNA', 'Mt_tRNA', 'miRNA', 'misc_RNA', 'rRNA', 'scRNA', 'snRNA', 'snoRNA', 'ribozyme', 'sRNA', 'scaRNA'] locate the TSS for each transcript get the regions (-200, 0) upstreaming of TSS |
cd script
./gtf_region.py
./gtf_region.py -h
usage: gtf_region.py [-h] [-g GTF_DIR] [-u GTF_URL] [-v GTF_VERSION] [-l GLEN]
[-w WINDOW_SIZE] [-b BED_DIR] [-r REGIONS [REGIONS ...]]
[-o OPEN_ACCESS_REGIONS [OPEN_ACCESS_REGIONS ...]]
optional arguments:
-h, --help show this help message and exit
-g GTF_DIR, --gtf_dir GTF_DIR
local directory for GTF file: only ENSEMBL or GENCODE GTF file accepted
-u GTF_URL, --gtf_url GTF_URL
specify URL to download GTF file. Use GENCODE by default
-v GTF_VERSION, --gtf_version GTF_VERSION
specify GTF release version to download
-l GLEN, --glen GLEN file for genome size
-w WINDOW_SIZE, --window WINDOW_SIZE
the value of w in calculating TSS regions. Default: 200
-b BED_DIR, --bed_dir BED_DIR
directory for output bed files
-r REGIONS [REGIONS ...], --regions REGIONS [REGIONS ...]
specify regions to generate bed files
-o OPEN_ACCESS_REGIONS [OPEN_ACCESS_REGIONS ...], --open_access_regions OPEN_ACCESS_REGIONS [OPEN_ACCESS_REGIONS ...]
specify regions to be included into open access tier
- You can find the generated bed files for Open-access Regions at your local folder
data/hg38/bed/gencode.v**/. E.g.,
data/hg38/bed
└── gencode.v38
├── cds.gencode_v38.20210915.bed.gz
├── control_access.gencode_v38.20210915.bed.gz
├── exon.gencode_v38.20210915.bed.gz
├── intron.gencode_v38.20210915.bed.gz
├── lncRNA.gencode_v38.20210915.bed.gz
├── lncRNA_promoter.gencode_v38.20210915.bed.gz
├── lncRNA_splice_site.gencode_v38.20210915.bed.gz
├── open_access.gencode_v38.20210915.bed.gz
├── protein_coding.gencode_v38.20210915.bed.gz
├── protein_coding_promoter.gencode_v38.20210915.bed.gz
├── protein_coding_splice_site.gencode_v38.20210915.bed.gz
├── smallRNA.gencode_v38.20210915.bed.gz
├── smallRNA_promoter.gencode_v38.20210915.bed.gz
├── smallRNA_splice_site.gencode_v38.20210915.bed.gz
├── utr3.gencode_v38.20210915.bed.gz
└── utr5.gencode_v38.20210915.bed.gz
- Here each genomic element has its own bed file for example:
exon.gencode_v**.{date}.bed.gz,smallRNA.gencode_v**.{date}.bed.gz,utr3.gencode_v**.{date}.bed.gzand etc. open_access.gencode_v**.{date}.bed.gzcontains the union of all the Open-access regions defined above.control_access.gencode_v**.{date}.bed.gzcontains the complementary regions of Open-access upon whole genome.- However ONLY
open_access.gencode_v**.{date}.bed.gzare kept in git.