Hi,
I want to get the coordinates of input file by extending 1000000bp up/downstream of TSS:
cat input.csv | awk 'NR>1{print $1"\t"$5"\t"$6}' | bedtools window -b stdin -a genes.bed -w 1000000 | awk 'OFS="\t" {print $6,$7,$8,$1,$2,$3,$4,$5}' >input_gene.bed #
Error: malformed BED entry at line 1635. Start Coordinate detected that is < 0. Exiting.
Hi, I want to get the coordinates of input file by extending 1000000bp up/downstream of TSS: cat input.csv | awk 'NR>1{print $1"\t"$5"\t"$6}' | bedtools window -b stdin -a genes.bed -w 1000000 | awk 'OFS="\t" {print $6,$7,$8,$1,$2,$3,$4,$5}' >input_gene.bed # Error: malformed BED entry at line 1635. Start Coordinate detected that is < 0. Exiting.
So how to set those negative values to 0? Best,