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sort the string which combined with string + numeric using bash script. $ sort -V #Sort #sort #number #string

Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

#Extract #Chromosome #Number And Start Position #Reads: samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

Count the number of sequences in fastaq file. grep -c '^@' sample1.fq #Fastaq #Count #Number #Grep #Dirty #Oneliner #NGS

To count number of fasta entries, I use: grep -c '^>' mySequences.fasta #Perl #Count #Number #Fasta #Linux #Grep

Count the number of "pattern" occurrence in a file grep -o 'pattern' anc.annots.gff | wc -l #Linux #grep #Count #Number #Occurrence

Count the total number of lines in a file. my $total=@{[<INFILE>]}; #Perl #Count #Number #Total #File