AWK-oneLiner

#### Deleting all folders in a dir
rm -R `ls -1 -d */`

for f in BedGraph/*.cov ; do  /home/ubuntu/bismark_v0.15.0/coverage2cytosine --genome_folder Wei_Genome/ -o $f BedGraph/$f; done

### Mapping DMCs to TAIR annotation and counting overlapping DRCs
bedtools intersect -a  LE_BB_DML.smooth.CHG.input -b ../FINAL_RESULTS/TAIR.allFeatures.sorted.checked -wb | awk '{ a[$8]++ } END { for (n in a) print n, a[n] }'

## Removing duplicated entries with same column values
 awk '!a[$1]++' 

## Sorting bed file
sort -V -k1,1 -k2,2  infile.bed > infile.sort.bed


### Getting important columns from pfam output file
awk  '{{for(i=23;i<=NF;++i) annotation =annotation " "  $i;} print $1 "\t" $2 "\t" $4 "\t" $7 "\t" $13 "\t" annotation ; annotation =""}' cicar.Eval10.pfam |sed 's/'\''//g'  > inputForExpTable

### Creating SQL command
awk -F "\t" -v q=\'  '{print "INSERT INTO  pfam_table (target, accession, query_name, Evalue_full, Evalue_domain, description ) values ( " q  $1 q ", " q $2 q ", " q  $3  q ", "   $4   ", "   $5   ", " q $6 q ");"}' inputForExpTable > SQL_commands_pfamTable