Normalization in Gene Expression Analysis

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What is the standard file format typically used to output gene expression data in RNA sequencing?

BAM

FASTQ

VCF

TSV (correct)

Which step in RNA sequencing involves organizing and tallying all reads mapped to a specific gene or transcript?

Allele fraction calculation

Alignment output

Gene count (correct)

Mutational effects prediction

What is the main goal of differential expression analysis in RNA sequencing?

Detecting anomalies in the reference genome

Predicting allele frequencies

Comparing gene expression levels between different conditions (correct)

Identifying mutations in the sample

Which type of file contains base call alignments to reference sequences in the context of RNA sequencing?

BAM Signup and view all the answers

What type of data can impact the calling of mutations in a sample during RNA sequencing?

Library preparation technique Signup and view all the answers

Which step is crucial for identifying anomalies that do not match the reference genome in RNA sequencing?

(Differential) expression data analysis Signup and view all the answers

What is the primary function of the secondary data analysis step in RNA-Seq?

To align reads to a reference transcriptome and quantify gene expression Signup and view all the answers

What is the purpose of the read cleanup step in RNA-Seq data analysis?

To remove low-quality sequence reads and trim low-quality bases Signup and view all the answers

Which of the following is an output of the demultiplexing step in RNA-Seq data analysis?

Multiple FASTQ files, each corresponding to a unique sample Signup and view all the answers

What is the purpose of sequence alignment in RNA-Seq data analysis?

To match each sequencing read to its corresponding location in the reference transcriptome Signup and view all the answers

What is the purpose of the Real-Time Analysis (RTA) software in RNA-Seq data generation?

To generate base calls and associated quality scores during sequencing Signup and view all the answers

Which of the following is not a primary processing step in RNA-Seq data analysis?

Sequence alignment to a reference transcriptome Signup and view all the answers

What is the purpose of normalization in RNA-Seq data analysis?

To account for technical biases and make gene expression levels comparable across samples Signup and view all the answers

Which software is commonly used for differential expression analysis in RNA-Seq?

Cufflinks Signup and view all the answers

What is the purpose of using different probability distributions in differential expression analysis?

To account for different types of biases in the data Signup and view all the answers

Which of the following is NOT a common challenge in RNA-Seq data analysis?

Aligning short reads to a reference genome Signup and view all the answers

What is the purpose of spiking in known quantities of nucleic acid in RNA-Seq experiments?

To serve as internal controls for normalization Signup and view all the answers

Which organization proposed a widely accepted nomenclature for reporting mutations or sequence variants?

Human Genome Variation Society (HGVS) Signup and view all the answers