This is a test version of Biostars. For the public version, visit https://www.biostars.org.
get genomic coordinates plus 5kb from Gene Symbols

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

genome mysql rmysql
• 2,603 views • link
updated by Chirag Nepal Chirag Nepal • written by jfertaj jfertaj

2 answers

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.

• 0 views • link
written by Ram Ram

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
• 0 views • link
updated by Ram Ram • written by Chirag Nepal Chirag Nepal

Log in to answer this question.

More posts like this