1) Print out the attributes column of a gff file
cut -f 9 ecoli.gff3
2) Find all genes in ecoli.gff3
grep "gene" ecoli.gff3 > genes_only.gff3 ## prints out every line that contains the word 'gene', saves those lines to a genes_only.gff3 file
grep -o "Name=[^;]\+" genes_only.gff3 ## prints out Name field for all genes in genes_only file
grep -e "gene" ecoli.gff3 | grep -o "Name=[^;]\+" ## to avoid creating a intermediate file (genes_only.gff3), you can use a pipe (more on this in the next section)
3) Print all the unique chromosomes in a bed file
cut -f 1 fileA.bed > fileA_chr_names.bed ## saves all chromosome names to a file
uniq fileA_chr_names.bed ## prints out unique chromosome names
cut -f 1 fileA.bed | uniq ## to avoid creating a intermediate file (fileA_chr_names.bed), you can use a pipe (more on this in the next section)