BMD 427 Lecture 7: RNA-seq Data Analysis
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Questions and Answers

What does the term 'transcriptome' refer to?

  • The collection of all transcripts, including mRNA, rRNA, tRNA, and ncRNA (correct)
  • The collection of ncRNA and mRNA transcripts only
  • The collection of all mRNA transcripts only
  • The collection of rRNA and tRNA transcripts only

    • What is the main purpose of RNAseq (or RNA-seq)?

  • To study the expression of only microRNAs
  • To analyze the structure of rRNA molecules
  • To obtain the transcriptional status of biological samples at a specific time (correct)
  • To sequence the entire genome of an organism

    • What types of reads are obtained from RNA-Seq?

  • mRNA Reads, rRNA Reads, Noncoding RNA (ncRNA) Reads
  • Intronic Reads, Splice Junction Reads, tRNA Reads
  • Exonic Reads, Exon–Intron Junction Reads, Poly(A) Reads (correct)
  • mRNA Reads, Small RNA Reads, Ribosomal RNA (rRNA) Reads

    • What is the read length range for RNA-Seq reads?

    <p>25–450 bp</p> Signup and view all the answers

    Which types of RNA are mainly studied using RNA-seq?

    <p>mRNA, Small RNA, Noncoding RNA (ncRNA), MicroRNAs</p> Signup and view all the answers

    What is the purpose of transcriptome sequencing?

    <p>To rapidly and comprehensively obtain the transcriptional status of biological samples at a specific time</p> Signup and view all the answers

    What is one of the crucial factors in RNAseq?

    <p>The number of sequenced reads for a given sample</p> Signup and view all the answers

    What is recommended regarding outliers with over 30% disagreement in raw reads?

    <p>They should be discarded</p> Signup and view all the answers

    What does the optimal library size depend on in RNAseq?

    <p>The complexity of the targeted transcriptome</p> Signup and view all the answers

    Which type of reads are preferable to characterize poorly annotated transcriptomes in RNA-seq?

    <p>Longer reads</p> Signup and view all the answers

    What is one of the quality-control checkpoints for raw reads in RNA-seq?

    <p>The overrepresented k-mers</p> Signup and view all the answers

    What varies with effect size, sequencing depth, and number of replicates in RNA-seq?

    <p>Statistical power to detect differential expression</p> Signup and view all the answers

    Which step involves obtaining raw reads, read alignment, and quantification in RNA-seq data acquisition?

    <p>Quality control</p> Signup and view all the answers

    What is crucial for proper sequencing and subsequent analysis in RNA-seq?

    <p>The optimal library size</p> Signup and view all the answers

    What should be homogeneous for samples in the same experiments in RNA-seq?

    <p>The overrepresented k-mers</p> Signup and view all the answers

    Which one of these is true about RNA-seq?

    <p>Longer reads are not preferable for characterizing poorly annotated transcriptomes.</p> Signup and view all the answers

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