BMD 427 Applied Bioinformatics Lecture 7: RNAseq Data Analysis

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What does the term 'transcriptome' refer to?

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

The collection of all mRNA transcripts only

The transcriptional status of biological samples at a specific time

The complete set of transcripts in a cell for a given physiological condition

What is the main purpose of RNA-seq?

To analyze small RNA or microRNAs

To study the ribosomal RNA (rRNA) and transfer RNA (tRNA)

To obtain the transcriptional status of biological samples at a specific time (correct)

To collect all types of RNA reads in a tissue or organism

Which types of reads are obtained from RNA-seq?

Exonic Reads, Exon–Intron Junction Reads, Poly(A) Reads (correct)

Long Sequences, Short Sequences, Medium Sequences

mRNA Reads, rRNA Reads, tRNA Reads

Small RNA Reads, Noncoding RNA Reads, MicroRNA Reads

What is the specific focus of RNA-seq in the study of biological samples?

mRNA Signup and view all the answers

What does WTSS stand for in the context of transcriptome sequencing?

Whole-Transcriptome Shotgun Sequencing Signup and view all the answers

What are the major types of RNA included in the transcriptome?

mRNA, rRNA, tRNA, ncRNA Signup and view all the answers

What is one of the crucial factors in RNA-seq?

Sequencing depth Signup and view all the answers

Which type of reads are preferable for characterizing poorly annotated transcriptomes?

Longer paired-end reads Signup and view all the answers

What is the size of the final fragments for Illumina sequencing?

Less than 500 bp Signup and view all the answers

What varies with effect size, sequencing depth, and number of replicates in detecting differential expression?

Statistical power Signup and view all the answers

What is recommended if outliers with over 30% disagreement are found in raw reads quality control?

They should be discarded Signup and view all the answers

Which checkpoints are used for quality control in RNA-seq?

Presence of adaptors, overrepresented k-mers, GC content Signup and view all the answers

What is one of the steps in the acquisition of RNA-seq data?

Raw reads QC Signup and view all the answers

What is crucial for proper sequencing and subsequent analysis?

$\text{Sequencing depth}$ Signup and view all the answers

'The best sequencing option depends on the analysis goals' - this statement refers to which factor affecting RNA-seq?

$\text{Experimental design}$ Signup and view all the answers

'More transcripts will be detected, and their quantification will be more precise as the sample is sequenced to a deeper level' - this statement refers to which factor affecting RNA-seq?

$\text{Sequencing depth}$ Signup and view all the answers

What is genome assembly?

The process of piecing together the DNA sequences of an organism's genome to create a comprehensive representation Signup and view all the answers

What makes genome assembly challenging?

Genome complexity, short reads, repetitive sequences, heterozygosity, and sequencing errors Signup and view all the answers

Why do short reads make the assembly process more challenging?

Short reads may make it impossible to resolve repetitive regions Signup and view all the answers

What complicates genome assembly due to its prevalence in many genomes?

Repetitive sequences Signup and view all the answers

In genome assembly, what does complexity refer to?

Repetitive sequences, structural variations, and varying ploidy levels Signup and view all the answers

What is the main purpose of genome assembly?

Creating a comprehensive representation of an organism's DNA sequences Signup and view all the answers

What is a challenge in determining where each read belongs in the assembly when they are identical or very similar?

Heterozygosity Signup and view all the answers

What is a potential issue introduced by sequencing technologies that can affect the accuracy of the assembly?

Base-calling errors Signup and view all the answers

Which assembly method represents reads as nodes and overlaps between reads as edges in a graph?

De Bruijn Graph-based Assembly Signup and view all the answers

Which assembly method is known for struggling with repetitive regions and being sensitive to sequencing errors?

De Bruijn Graph-based Assembly Signup and view all the answers

Which assembly approach uses pairwise read alignments to identify overlaps between reads and is effective for long-read data?

DNA Overlap-Layout-Consensus (OLC) Assembly Signup and view all the answers

Which method aims to order and orient contigs to create larger genomic segments after initial assembly?

Scaffolding Signup and view all the answers

What is a strength of the Scaffolding method in genome assembly?

Improves the continuity and contiguity of genome assemblies Signup and view all the answers

What is a limitation of the Overlap-Layout-Consensus (OLC) Assembly method?

Computationally intensive and slower Signup and view all the answers