How to get exon coordinates in BED format?

Calendar 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.

How To Get Chromosome Position Given Rs Number?

Calendar February 27, 2021
Application
Primer Design, Multiplex PCR, Bioinformatics, SNP

Introduction#

We have a list of SNP rs numbers, like:

rs1002315756
rs1003815568
rs1004109382
rs1004635980
rs1008829651

And we want the genome positions for each SNPS, the results should like:

#chrom	chromStart	chromEnd	name	ref	altCount	alts	shiftBases	freqSourceCount	minorAlleleFreq	majorAllele	minorAllele	maxFuncImpact	class	ucscNotes	_dataOffset	_dataLen
chr1	51453	51454	rs1004109382	C	1	T,	0	0				0	snv	rareSome,rareAll,	409400514	36
chr1	51594	51599	rs1004635980	GGGGG	1	GGGG,	4	12	-inf,-inf,0.000127421,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,	,,GGGGG,,,,,,,,,,	,,GGGG,,,,,,,,,,	0	delins	rareSome,rareAll,overlapDiffClass,	461755619	105
chr1	10042	10043	rs1008829651	T	1	A,	0	0				1986	snv	rareSome,rareAll,	878656298	46
chr1	10320	10321	rs1002315756	C	1	T,	0	12	-inf,-inf,-inf,-inf,-inf,0.00102617,-inf,-inf,-inf,-inf,-inf,-inf,	,,,,,C,,,,,,,	,,,,,T,,,,,,,	1986	snv	rareSome,rareAll,overlapDiffClass,	230771761	107
chr1	52763	52764	rs1003815568	T	1	A,	0	0				0	snv	rareSome,rareAll,	380161821	36

Method#

UCSC Table Browser do this job perfectly, thanks.