Common gene names list to BED with +/- TSS intervals

Question

[rbronste]

Just trying for simplest way to take a set of common gene names and generate a bed interval file of +/- 2kb of each gene TSS? Thanks.

[GenoMax]

Are answers here not extendable to current question: Table browser +/- 2Kb of TSS export You had asked this question back then.

[rbronste]

Yes its helpful but I was looking for best conversion method of common gene names to RefSeq or UCSC etc outside of Table Browser which appears to be lacking in this respect.

[GenoMax]

conversion method of common gene names to RefSeq or UCSC

That is a different question then. I would suggest taking a look at this file.

Answer 1

[Alex Reynolds]

If you have file of mouse gene symbols called genes.txt, here's one way you might get mouse gene 2kb proximal promoters for mm10 or GRCm38:

$ wget -qO- ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M18/gencode.vM18.annotation.gff3.gz \
    | gunzip --stdout - \
    | awk '$3 == "gene"' - \
    | convert2bed -i gff - \
    | awk -vwindow=2000 -vOFS="\t" '($6=="+"){ print $1, ($2 - window), $2, $4, ".", $6, $7, $8, $9, $10 }($6=="-"){ print $1, $3, ($3 + window), $4, ".", $6, $7, $8, $9, $10 }' \
    > gencode.vM18.promoters.bed

Then to filter them against the list of genes:

$ grep -w -F -i -f genes.txt gencode.vM18.promoters.bed > gencode.vM18.promoters.filtered.bed

[rbronste]

Very late reply, but this gets only upstream of the TSS by 2kb, wondering how I can get a window of 2kb on either side? Thanks!

[Alex Reynolds]

Modify both start and pesudo-stop?

$ wget -qO- ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M18/gencode.vM18.annotation.gff3.gz \
    | gunzip --stdout - \
    | awk '$3 == "gene"' - \
    | convert2bed -i gff - \
    | awk -vwindow=2000 -vOFS="\t" '($6=="+"){ print $1, ($2 - window), ($2 + window), $4, ".", $6, $7, $8, $9, $10 }($6=="-"){ print $1, ($3 - window), ($3 + window), $4, ".", $6, $7, $8, $9, $10 }' \
    | awk -vOFS="\t" '{ if ($2 < 0) { $2 = 0; } print $0; }' \
    > gencode.vM18.promoters.bed

I added a test, to adjust the start coordinate to zero if it is less than zero. You might instead filter these elements out, if you require all elements to be 4kb windows centered on their TSSs.