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Question: Common gene names list to BED with +/- TSS intervals
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gravatar for rbronste
7 months ago by
rbronste • 230
rbronste • 230 wrote:

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.
rna-seq • 318 views
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modified 7 months ago by Alex Reynolds ♦ 27k • written 7 months ago by rbronste • 230
1

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

ADD REPLY • link modified 7 months ago • written 7 months ago by genomax ♦ 64k

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.

ADD REPLY • link written 7 months ago by rbronste • 230

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.

ADD REPLY • link written 7 months ago by genomax ♦ 64k
0
gravatar for Alex Reynolds
7 months ago by
Alex Reynolds ♦ 27k
Seattle, WA USA
Alex Reynolds ♦ 27k wrote:

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
ADD COMMENT • link written 7 months ago by Alex Reynolds ♦ 27k
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