get genomic coordinates plus 5kb from Gene Symbols

Question

[jfertaj]

Hi list,

I am trying to use RMySQL to get genomic coordinates from a bunch of gene symbols and add 5kb to the TSS afterwards. I know I can do it using Tables from UCSC browser or BiomaRt but I would like to learn how to query using RMySQL or mysql,

I have followed this post but I cannot figure out how to do it with geneSymbols (HUGO names) because name in Knowngene table is different from kgXref table

Any help would it be appreciated

Thanks

Answer 1

[Ram]

Use a join with knownGene.name=kgXref.kgID

You can always use the Table Browser to check the schema of UCSC's MySQL tables to guess which identifiers might match. These tables are highly redundant to help querying, mapping and display.

Answer 2

[Chirag Nepal]

If interested, another alternative way is to use one-liner:

Extract 5KB region around TSS

cat input.bed | awk 'BEGIN {OFS="\t"}  { if ($6 == "+") { print $1,$2-5000,$2+5000,$4,$5,$6 } else if ($6 == "-") { print $1,$3-5000,$3+5000,$4,$5,$6 } > Temp

If you want sequence of these: used bedtools

fastaFromBed -s -name -fi assembly.fa -bed Temp -fo Temp.fa