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BMD 427 Lecture 7: RNA-seq Data Analysis

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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?

25–450 bp (B) Signup and view all the answers

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

mRNA, Small RNA, Noncoding RNA (ncRNA), MicroRNAs (D) Signup and view all the answers

What is the purpose of transcriptome sequencing?

To rapidly and comprehensively obtain the transcriptional status of biological samples at a specific time (D) Signup and view all the answers

What is one of the crucial factors in RNAseq?

The number of sequenced reads for a given sample (D) Signup and view all the answers

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

They should be discarded (C) Signup and view all the answers

What does the optimal library size depend on in RNAseq?

The complexity of the targeted transcriptome (C) Signup and view all the answers

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

Longer reads (B) Signup and view all the answers

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

The overrepresented k-mers (C) Signup and view all the answers

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

Statistical power to detect differential expression (A) Signup and view all the answers

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

Quality control (D) Signup and view all the answers

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

The optimal library size (A) Signup and view all the answers

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

The overrepresented k-mers (D) Signup and view all the answers

Which one of these is true about RNA-seq?

Longer reads are not preferable for characterizing poorly annotated transcriptomes. (A) Signup and view all the answers