Change Chromosomal Position To Gene Sequence Position (Mutations)

Question

[Stephan]

I have a list of mutations with their chromosomal locations like chr1:6266188-6266188 chr22:5443534-5443534 .....

I know how to fetch a list of genes with ucsc browser and/or galaxy that intersects with my mutations. and their accompanying DNA sequence

But I want to fetch the gene sequence with the mutations highlighted or the position in uppercase or just the location IN the gene. so that I can easy invistigate what kind of mutation it is. And just the position in the gene

i know chromosomal position , but a fasta sequence always begins with position 1 to whatever. they don't start with lets say 6266100

dream result would be: gene blabla lenght: 1...789 your mutation is in place 88 of the sequence or actaGacta or actaNacta

hope you'll understand thanks

Answer 1

[Pierre Lindenbaum]

Use the UCSC KnownGene table to build the sequence of the cDNA(s) by walking over the exons: just like it was described here: A: Amino Acid Position In Ucsc Browser