Question

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

0

Entering edit mode

4.0 years ago

mathavanbioinfo ▴ 80

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

RNA-Seq lncRNA target genes upstream downstream • 1.4k views

ADD COMMENT • link updated 12 months ago by SeguraChain • 0 • written 4.0 years ago by mathavanbioinfo ▴ 80

0

Entering edit mode

Hi,

What is the purpose of the gene rs11098403 ? I'm afraid once I read 300kb/s upstream, it's like downloading/uploading meaning.

Thank you.

ADD REPLY • link 12 months ago by SeguraChain • 0

score 1 · Answer 1 · 2020-11-30

1

Entering edit mode

4.0 years ago

ATpoint 85k

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.

ADD COMMENT • link 4.0 years ago by ATpoint 85k

score 1 · Answer 2 · 2020-11-30

1

Entering edit mode

4.0 years ago

JC 13k

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

ADD COMMENT • link 4.0 years ago by JC 13k