Bioinformatics

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. ...

How To Get Chromosome Position Given Rs Number?

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. ...