Downloading genomic interval for hg38
3
0
Entering edit mode
4.4 years ago
ChIP ▴ 590

Hi,

I want to download genomic information for hg38, that have following information:

region gene exon/tss/intron/intergenic/CpG/nonCpG

The idea is to get this in a table format and then use intersectBed to to get overlap between the ChIP-seq data and this genomic information file.

How can I get this information. The CpG information is important as I have methylation data.

Thank you

ChIP-Seq • 2.5k views
ADD COMMENT
1
Entering edit mode

Hi, please look at UCSC genome browser and select table - you can get print all required informations.

ADD REPLY
3
Entering edit mode
4.4 years ago

GENCODE release 26 offers some of these annotations for hg38. Pipe to BEDOPS gff2bed to make a sorted BED file.

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/gencode.v26.annotation.gff3.gz | gunzip -c - | gff2bed - > gencode.v26.bed

For hg38, you can grab the cpgIslandExt table from UCSC's goldenpath service, and use BEDOPS sort-bed to build a sorted BED4+ file:

$ wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cpgIslandExt.txt.gz \
   | gunzip -c - \
   | awk 'BEGIN{ OFS="\t"; }{ print $2, $3, $4, $5$6, substr($0, index($0, $7)); }' - \
   | sort-bed - \
   > cpgIslandExt.hg38.bed

Derived from the table schema for this file, the first four columns are the island's genomic interval and name. The remaining columns are island length, number of CpGs in the island, the number of C and G in the island, the percentage of island that is CpG, the percentage of island that is C or G, and the ratio of observed(cpgNum) to expected(numC*numG/length) CpG in island.

Once you have these files in sorted BED format, you can start doing set operations and mapping with BEDOPS bedops and bedmap etc.

ADD COMMENT
2
Entering edit mode
4.4 years ago
shwethacm ▴ 230

UCSC table browser has what you need (and more! ) https://genome.ucsc.edu/cgi-bin/hgTables

(( PS: CpG information is under group:Regulation ))

ADD COMMENT
1
Entering edit mode
4.4 years ago
Ming Tang ★ 2.7k

see http://crazyhottommy.blogspot.com/2016/11/define-intronic-exonic-and-intergenic.html it is for hg19, but you can just change to hg38.

ADD COMMENT

Login before adding your answer.

Traffic: 1565 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6