How to get exon coordinates in BED format?

How to get exon coordinates in BED format?

December 20, 2023
Application
Primer Design, Multiplex PCR, Bioinformatics, Gene

Introduction #

We have a list of genes, like:

EGFR
MET
TP53

And we want the genome positions plus 10 bases at each end for each exons, the results should like:

chr7	116672185	116672587	NM_000245_exon_0_10_chr7_116672196_f	0	+
chr7	116699060	116700294	NM_000245_exon_1_10_chr7_116699071_f	0	+
chr7	116731657	116731869	NM_000245_exon_2_10_chr7_116731668_f	0	+
chr7	116739939	116740094	NM_000245_exon_3_10_chr7_116739950_f	0	+
chr7	116740841	116741035	NM_000245_exon_4_10_chr7_116740852_f	0	+
chr7	116755344	116755525	NM_000245_exon_5_10_chr7_116755355_f	0	+
chr7	116757426	116757549	NM_000245_exon_6_10_chr7_116757437_f	0	+
chr7	116757627	116757784	NM_000245_exon_7_10_chr7_116757638_f	0	+
chr7	116758448	116758630	NM_000245_exon_8_10_chr7_116758459_f	0	+
chr7	116759380	116759500	NM_000245_exon_9_10_chr7_116759391_f	0	+

Method #

UCSC Table Browser do this job perfectly, thanks.

  1. Visit: https://genome.ucsc.edu/cgi-bin/hgTables.
  2. On the “Table Browser” page, select proper parameters. Get Exon BED Step 1
  3. Click “paste list” and paste gene list as following picture shows, , then click “submit”. Get Exon BED Step 2
  4. Select “Exons” plus “10” bases, then click “get BED” Get Exon BED Step 3
  5. We get the genome positions as expected, done. Get Exon BED Step 4