Project brief
A hypothetical FASTQ file contains three reads with sequences ACGTACGT, ACGTA and ACGT. Their quality strings are IIIIIIII, IIIII and !!!!, respectively.
Your tasks
- Calculate the length of each read.
- Identify which read has the lowest base-call quality.
- Explain why quality control should take place before read alignment.
Expected submission
Prepare a three-row table containing each read’s length and a brief quality assessment. Add a short interpretation, then open the worked-solution section to compare your result.
View the project solution +
Read lengths: 8, 5 and 4 nucleotides.
Quality: In common Phred+33 encoding, I corresponds to Q40 and ! to Q0. The third read therefore has extremely low quality.
Quality checks before alignment help identify problematic reads and guide trimming or filtering decisions. Real datasets require assessment of the full quality report, rather than just one read.