How to identify the 300 kb upstream and downstream genes of lncRNAs?

Question

[mathavanbioinfo]

Hi I have a list of human lncRNAs expressed in the blood sample. I want to know the upstream and downstream of genes in the range of ± 300 kb. please guide me on how to find out.

---

lncRNAs ENSG00000269794, ENSG00000273472 ENSG00000279066 ENSG00000279926 ENSG00000280047 ENSG00000280184 ENSG00000286162

Answer 1

[ATpoint]

Get their start coordinate, use bedtools slop to extend the coordinate to both direction to get your desired window, then use bedtools intersect to intersect that output with any gene coordinates you like.

Answer 2

[JC]

Use biomart https://www.ensembl.org/biomart/martview