Page Comparison

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Based on the library preparation, we expect that our forward reads were cut with the restriction enzyme nlaIII (NLA3).

We expect that the vast majority of our reads should have the recognition sequence in them.

3. How can we check that our reads largely fit this expectation? (Hint: we'll need to know the restriction enzymes recognition sequence)

#Looking up nlaIII, we see it's cut site:
#     CATG'
#    'GTAC
  
#check if we see this cut site in the forward reads
grep CATG Lib01_R1.fastq | wc -l


#compare with total read count
expr $(cat Lib01_R1.fastq | wc -l) / 4

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