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#This library was prepared with bcgl restriction enzyme
#Check that the cut site appears in the reads
#How many reads do we have?
expr $(cat A_CTGCAG_R1.fastq | wc -l) / 4
expr $(cat B_GAAGTT_R1.fastq | wc -l) / 4
	#7011846
 
#How many of the reads have the cut site?
grep "CGA......TGC" A_CTGCAG_R1.fastq | wc -l
	#3429158
 
#3429158/7011846 = 0.49
#Why is the cut site only in half the reads?
 
#This occurs because during the 2bRAD library prep
#the adapters can be ligated to the fragment in either
#orientation (note the mirrored sticky ends left by bcgl).
#So the genomic fragment may have been read from either direction
 
#check for reverse complement of cut site
grep "GCA......TCG" A_CTGCAG_R1.fastq | wc -l
	#3274171
 
#(3429158 + 3274171) / 7011846 = 0.96
#Good, as expected the vast majority of the reads have the cut site.
#These look like 2bRAD reads