how to get percent identity between two RNA-seq fastq files?

Question

[lkianmehr]

Hello, Does anybody have an idea about the way to get percent identity between two or more RNA-seq fastq files ? or to show how many of the sequences in one of them are found in another one?

thanks in advance

Answer 1

[Pierre Lindenbaum]

 comm \
     <(gunzip  -c 11.fq.gz | paste - - - - | cut -f 2 | sort)  \
     <(gunzip  -c f2.fq.gz | paste - - - - | cut -f 2 | sort) | \
     awk -F '\t' '{if($1=="" && $2=="") {C+=1.0;};} END {print C/NR;}'

[lkianmehr]

I have run that command on two fastq files that are sequenced on the same library, I got one value = 0.119817, what does it mean? it means they have just 0.1 percent difference?

[Pierre Lindenbaum]

1/10 of reads in common.