Does it possible to know what are the adjacent genes up to 1000bp upstream and downstream of IS element

Question

[Neel]

Hi, i want to know what are IS/transposable element are present up to 100/1000 bp of upstream and downstream of my interest of genes . How to do that, does anyone know anything please let me know. It will be big help for me.

Thank you!

Answer 1

[Trivas]

Look into bedtools window command. See https://bedtools.readthedocs.io/en/latest/content/tools/window.html. Should be pretty straight forward from there.

[Neel]

Thank you for your reply...

Answer 2

[Alex Reynolds]

You could use bedmap from BEDOPS. Say you have a BED file of IS/transposable elements called elements.bed and a BED file of genes called genes.bed:

$ bedmap --echo --range 1000 --delim '\t' elements.bed genes.bed > answer.bed

The file answer.bed will have, on each line, a IS/transposable element and any genes which overlap a window 1kb upstream and downstream of the element's edges.

If you need genes in BED format and you are starting with annotations in GFF or GTF format, you can use gff2bed or gtf2bed, e.g.:

$ wget http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gtf.gz
$ gtf2bed < <(zcat Homo_sapiens.GRCh38.106.chr.gtf.gz) > Homo_sapiens.GRCh38.106.chr.bed

Or to avoid generating an intermediate file:

$ wget -qO- http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.chr.gtf.gz | gunzip -c | gtf2bed - > Homo_sapiens.GRCh38.106.chr.bed

[Neel]

Thank You Sir for your reply.