Obtaining .bed list of exons of chr17
I would like to download/build a simple .bed file with all the exon regions oh chr17. Can anyone help me with that?
Thank you in advance.
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Via BEDOPS convert2bed:
$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/GRCh37_mapping/gencode.v26lift37.annotation.gff3.gz \
| gunzip --stdout - \
| awk '$3 == "exon"' - \
| convert2bed -i gff - \
> exons.bed
Then you can use BEDOPS bedextract to quickly get a subset:
$ bedextract chr17 exons.bed > exons.chr17.bed
This does a binary search through the sorted exons.bed file to get the chromosome you want, and will work much faster than a naive, linear walk through the file.
If you really just want chr17 and don't care about the rest:
$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/GRCh37_mapping/gencode.v26lift37.annotation.gff3.gz \
| gunzip --stdout - \
| awk '($3 == "exon") && ($1 == "chr17")' - \
| convert2bed -i gff - \
> exons.chr17.bed
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duplicate of Exon Coordinates Of Hg19 Genome Download