TSS +/- N bp from GTF > BED6

getTSS.sh

#!/bin/bash

BEDTOOLS=/usr/bin/bedtools/bin
ODIR=/data/dbase/

GENOME=hg19
SLOP=3000
SLOP_OPTS='-l 3000 -r 3000'
GENE_BED=${IDIR}/${GENOME}_3kb.bed

## NOTE: does not account for multiple transcripts; use uniqueGenes.R to collapse to min start/max end
####
if [ ${GENOME} == "hg19" ];then
	GTF=/data/dbase/human/hg19/gencode.v19.annotation.gtf
	CHR_LEN=/data/dbase/human/hg19/hg19_chr.len
elif [ ${GENOME} == "mm10" ];then
	GTF=/data/dbase/mouse/mm10/Mus_musculus.GRCm38.90.gtf
	CHR_LEN=/data/dbase/mouse/mm10/mm10.chrom.sizes
else
	die "genome not supported"
fi

## Extract TSS coordinates for fwd strand genes
grep -w transcript ${GTF} | awk '$7=="+"' |\
cut -d '"' -f-2,10 | cut -f1,4,5,9 | sed 's/gene_id "//' |\
tr '"' '_' | awk '{OFS="\t"} {print $1,$2,$2,$4,$5,$6}' > ${DIR}/tmp+

## Extract TSS coordinates for reverse strand genes
grep -w transcript ${GTF} | awk '$7!="+"' |\
cut -d '"' -f-2,10 | cut -f1,4,5,9 | sed 's/gene_id "//' |\
tr '"' '_' | awk '{OFS="\t"} {print $1,$3,$3,$4,$5,$6}' > ${DIR}/tmp-

## $4=ensembl id, $5=name
cat ${DIR}/tmp+ ${DIR}/tmp- | ${BEDTOOLS} slop -i - -g ${CHR_LEN} ${SLOP_OPTS} | sort -k1,1 -k2n,2 |\
awk '{OFS="\t"} {print $1,$2,$3,$4,$5,$6}' | sed 's/_/\t/' | cut -f 4 --complement > ${DIR}/${BED}

rm ${DIR}/tmp*