Question: how to get percent identity between two RNA-seq fastq files?
0
gravatar for lkianmehr
3 months ago by
lkianmehr30
France
lkianmehr30 wrote:

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

rna-seq percent identity • 154 views
ADD COMMENTlink modified 3 months ago by Pierre Lindenbaum118k • written 3 months ago by lkianmehr30
0
gravatar for Pierre Lindenbaum
3 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:
 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;}'
ADD COMMENTlink written 3 months ago by Pierre Lindenbaum118k

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?

ADD REPLYlink modified 3 months ago • written 3 months ago by lkianmehr30

1/10 of reads in common.

ADD REPLYlink written 3 months ago by Pierre Lindenbaum118k
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