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How to get coordinate of genomic elements?

Hi everyone,

I need coordinate of following genomic elements in hg38 version.

  1. Promoter
  2. Enhancers
  3. Exon
  4. Intron
  5. 5'UTR
  6. 3'UTR
  7. Intergenic
  8. CDS
  9. LINEs
  10. SINEs
  11. LTRs
  12. N and S shores
  13. N and S shelves
  14. CpG island
  15. Transposons

If anyone can provide leads for even some of the features, please give your suggestions.

Thanks

repeats promoter enhancer cpg
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written by Ankit Ankit

I used this package annotatr for genomic features:

For repeats, I obtained list from SQL table

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written by Ankit Ankit

Promoter http://ftp.ensembl.org/pub/release-104/regulation/homo_sapiens/RegulatoryFeatureActivity/; annotatr

Enhancers http://ftp.ensembl.org/pub/release-104/regulation/homo_sapiens/RegulatoryFeatureActivity/;

https://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/extra/enhancer/; annotatr

Exon annotatr

Intron annotatr

5'UTR annotatr

3'UTR annotatr

Intergenic annotatr

CDS annotatr

LINEs http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/rmsk.txt.gz

SINEs http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/rmsk.txt.gz

LTRs http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/rmsk.txt.gz

N and S shores annotatr

N and S shelves annotatr

CpG island Table_Browser -> Regulation->CpG Islands; annotatr

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written by Ankit Ankit

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