My goal is to compare reads from two different fastq files on a Linux machine. The following are the comparisons to perform:
- How many common reads are between the two fastq files?
- How many reads are present in one fastq file that are not present in the other? i.e reads that are unique to each file.
- Where and how do the sequences differ in both files? Is there a difference in nucleotide base at the end of the sequence(3' end), the start of the sequence(5'end) or is it somewhere in the middle of the sequence? Is there a difference in length of the sequence? If so, what is the length and what is the difference? I would like to get the original sequences plus the difference between them for analysis.
- Does the quality score differ? Where and how do the quality of sequences differs?
Any guidance regarding how to approach this question is very appreciated.
Edit: I'm working on paired-end reads from the same individual. What I want to do is to compare different trimming tools from their output.