Finding if genes present in a gene list intersect genomic intervals

Question

[alexmondaini]

Suppose I have a bed file that looks like that:

chr19   3963597 3963614 15.6239329995745    5.03285901269881    -
chr19   3963614 3963617 5.86660801019953    4.6301105247803 -
chr19   3963576 3963597 12.0356036427941    3.87189496525513    -
chr19   3963569 3963572 12.0356036427941    3.87189496525513    -

And I also have a gene list that looks like this:

PTPRN2
ANP32A
SKI
WDR33
MAGI1
TF
CMIP

What is the best way to find if the gene names are inside the genomic intervals of my bed file ?

Thanks in advance.

[Pierre Lindenbaum]

convert gene to coordinate (e.g using biomart) Get genomic coordinates from gene names, From gene symbol list to their coordinates ; and then use bedtools intersect