find long coding RNA's up and downstream genes

Question

[newbiebio]

Known lncRNA's location. How to find their up and downstream genes? By UCSC, R(TxDb.Hsapiens.UCSC.hg38.knownGene) package or bedtools?

[WouterDeCoster]

Could you be more informative with regard to which data you have and what you aim to obtain?

[newbiebio]

Hello, I have a lncRNA and know it's chromosome, genomic start and end coordinate. Right now, I am trying to extract all the known genes from UCSC,hg38.

[WouterDeCoster]

Try to be as informative as possible when asking questions.

Can you clarify what you mean with an up and downstream gene? Is it in a pathway, functionally, or the genomic coordinates, the location?

UCSC has a table browser which should allow you to extract "the known genes".

[newbiebio]

Hello, I got some lncRNAs, ex. TP4 chr4 10001(start position) 101030(end position). I need to find all the genes that located within 2000 bp of lncRNA's upstream and downstream. Thank you.

[WouterDeCoster]

I would use bedtools annotate or similar for this, make a bed file containing (for your example):

chr4 80001 10001 TP4_up
chr4 101030 103030 TP4_down

And annotate that with all genes