Exome.bed for hg19

Question

[john]

where can I get an exome.bed file for hg19 that simply lists all the coding regions?

[cpad0112]

try table browser from UCSC.

Answer 1

[Pierre Lindenbaum]

here, for example. The information is included in the definition of the transcipts.

transcript ENST00000456328 has 3 exons: first exon starts at 11868 and ends(excluded) at 12227 , last exon starts at 13220 and ends at 14409

$ wget -q -O - "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz" | gunzip -c | head -n 1 | tr "\t" "\n" | nl
     1  585
     2  ENST00000456328.2
     3  chr1
     4  +
     5  11868
     6  14409
     7  11868
     8  11868
     9  3
    10  11868,12612,13220,
    11  12227,12721,14409,
    12  0
    13  DDX11L1
    14  none
    15  none
    16  -1,-1,-1,

schema in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.sql

you can use awk to convert this to a BED file. see How to find the amino acid residue that is encoded by codon which is encoded by two different adjacent exons