Sanger Sequencing Steps: DNA Polymerase Synthesis
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Questions and Answers

What is the default file format generated by sequencers in NGS?

  • BAM
  • VCF
  • FASTQ (correct)
  • FASTA

    • Why is the .bcl format generated by Illumina-based NGS machines not useful?

  • It is incompatible with the sequencing machine
  • It is not a text-based format
  • It lacks quality scores (correct)
  • It cannot store raw sequence data

    • What is the purpose of converting BCL files to FASTQ files in NGS?

  • To improve sequencing speed
  • To reduce file size
  • To increase the accuracy of base calls
  • To make the data compatible for secondary analysis (correct)

    • What information is stored for each read in a FASTQ file?

    <p>Raw sequence data and quality scores (A)</p> Signup and view all the answers

    Which NGS systems provide the option to automatically convert BCL files to FASTQ format?

    <p>MiniSeq and MiSeq (C)</p> Signup and view all the answers

    What is the primary advantage of using FASTQ files over .bcl files in NGS?

    <p>.bcl files cannot be used for secondary data analysis (B)</p> Signup and view all the answers

    What is the purpose of the 'Sequence' element in the text?

    <p>To act as a placeholder for the base qualities (B)</p> Signup and view all the answers

    What is the relationship between the quality score Q and the probability P that a base call is incorrect?

    <p>Q is a logarithmic function of P (A)</p> Signup and view all the answers

    What is the purpose of multiplying log10P by -10 in the formula for Q?

    <p>Both a and b (B)</p> Signup and view all the answers

    What is the purpose of the Phred+33 encoding scheme?

    <p>All of the above (D)</p> Signup and view all the answers

    What is the quality score corresponding to a probability P of 0.01?

    <p>20 (D)</p> Signup and view all the answers

    What is the quality score corresponding to a probability P of 0.4?

    <p>-0.398 (D)</p> Signup and view all the answers

    What is the primary purpose of raising the temperature after the primer has bound in Sanger sequencing?

    <p>To allow DNA polymerase to synthesize new DNA from the primer (C)</p> Signup and view all the answers

    What is the role of dideoxy nucleotides (ddNTPs) in Sanger sequencing?

    <p>They terminate the DNA synthesis process when incorporated (A)</p> Signup and view all the answers

    What is the purpose of repeating the Sanger sequencing process in multiple cycles?

    <p>To ensure that a dideoxy nucleotide is incorporated at every position of the target DNA (D)</p> Signup and view all the answers

    What is the purpose of gel electrophoresis in Sanger sequencing?

    <p>To separate the DNA fragments based on their length (B)</p> Signup and view all the answers

    In contrast to Sanger sequencing, what is a key advantage of Next-Generation Sequencing (NGS) technology?

    <p>It allows for the parallelized sequencing of the entire genome at once (C)</p> Signup and view all the answers

    What is the first step in the NGS workflow mentioned in the text?

    <p>DNA sample preparation (D)</p> Signup and view all the answers

    What is the purpose of the QtoPhred33 function?

    <p>To convert an integer quality score to the corresponding ASCII-encoded character (B)</p> Signup and view all the answers

    What is the purpose of the Phred33toQ function?

    <p>To convert an ASCII-encoded quality character to the corresponding integer quality score (D)</p> Signup and view all the answers

    What is the expected output for the average quality score calculation in Exercise 3?

    <p>The sequence and average quality score for each read in the FASTQ file (A)</p> Signup and view all the answers

    Which of the following is NOT a topic covered in the references provided?

    <p>FASTQ file format and Phred quality scores (B)</p> Signup and view all the answers

    What is the purpose of the chr() function in the QtoPhred33 function?

    <p>To convert an integer to a character according to the ASCII table (B)</p> Signup and view all the answers

    What is the purpose of the ord() function in the Phred33toQ function?

    <p>To convert a character to an integer according to the ASCII table (B)</p> Signup and view all the answers

    What is the purpose of the Phred33ToQ function?

    <p>To convert a Phred quality score to an ASCII-encoded quality score (D)</p> Signup and view all the answers

    In the given code, what does the createHist function return?

    <p>A dictionary of base quality frequencies (C)</p> Signup and view all the answers

    What is the purpose of the random.choice function in the provided code?

    <p>To generate a random DNA sequence (C)</p> Signup and view all the answers

    What is the purpose of the ord function in the Phred33ToQ function?

    <p>To convert a character to its ASCII value (A)</p> Signup and view all the answers

    What is the purpose of the range(len(hist)) expression in the plotting code?

    <p>To generate a list of x-axis values for the histogram (B)</p> Signup and view all the answers

    What is the purpose of the exercise at the end of the provided code?

    <p>To parse a FASTQ file and store the reads and qualities in separate lists (B)</p> Signup and view all the answers

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