1) Replace all the tabs in fileA.bed with commas
sed -e 's/\t/,/g' fileA.bed ## add the trailing /g for 'global' replacement (all matching occurrences)
2) Convert SRR2014925_1.fastq into a FASTA file
sed -n '1~4s/^@/>/p;2~4p' SRR1570041_1.fastq > SRR1570041_1.fa
3) Transform ecoli.gff3 into a BED file
grep -v "#" ecoli.gff3 | grep -v "CDS" | awk '{ print $1, $4-1, $5-1, $9, $6, $7 }'
## need to filter out '#' lines at the beginning and 'CDS' lines which have an inconsistent number of columns
4) Calculate the average sequence depth for NZ_CP013025.1 from SRR2014925.bedgraph
grep "NZ_CP013025.1" SRR2014925.bedgraph | awk 'BEGIN { SUM=0; } { SUM+=$4; print $0 } END { print "Total = "SUM/NR }'