Week 7 Flashcards
Splice-aware aligner is needed when -
A. Mapping RNA-seq reads to detect exon-exon junctions.
B. Aligning DNA-seq reads for SNP discovery.
C. Detecting alternative splicing events in transcript alignment.
D. Analyzing structural variants in whole-genome sequencing.
E. Performing de-novo genome assembly.
A and C
Which of the following statements about HISAT2 algorithm is correct?
A. HISAT2 algorithm only uses BWT indexing for constructing its indexes.
B. HISAT2 algorithm uses FM indexing but not BWT indexing for constructing its indexes.
C. HISAT2 algorithm is a splice-aware aligner and it uses a combination of BWT and FM
indexing to construct its indexes.
D. HISAT2 algorithm include a module for SNP calling.
E. HISAT2 algorithm uses BWT for SNP calling.
C and D
What kind of structural variation is this?
A. Paired duplication inversion
B. Paired insertion duplication
C. Paired duplication
D. Paired flanked inversion
A
Which of the tool(s) use the read pair distance method for identification of structural variants?
A. Samtools
B. Bcftools
C. BreakDancer
D. Pindel
E. PEMer
C and E
Which of the methods is/are particularly effective for detecting small structural variants whose
breakpoint is located within repetitive or complex genomic regions?
A. Split read methods.
B. Assembly based methods.
C. Read - pair distance method
D. Read - depth methods
A and B
What are the files that are required as inputs in the featureCounts algorithm?
A. BAM and GFF
B. SAM and SAF
C. SAM and GFF
D. SAM and VCF
E. BAM and VCF
A B and C
Identify the true statement(s) about copy number variation (CNV)?
A. CNV occurs when there are changes in the order of DNA segments in the genome.
B. CNV is a part of structural variations that involve gain or loss of a specific DNA
fragment
C. CNV can occur only at coding regions in the genome as they code for proteins.
D. Read depth variations from the anticipated copy number may be a sign that CNVs are
present
B and D
What happens due to alternate splicing?
Which of the processes is generally responsible for generation of mRNA isoforms?
A. Alternative polyadenylation
B. Intron retention.
C. Post transcriptional gene silencing
D. Alternative Splicing
E. Alternative cleavage.
A D E
Which of the following option(s) are the advantages of long-read direct RNA sequencing?
A. Can detect RNA modifications
B. It is not a sequencing by synthesis process.
C. It has the best accuracy.
D. Is able to identify isoforms.
A B D
Identify the true statement(s) from the following.
A. Insertion, Inversion, and translocations are different types of non-CNV structural
variants.
B. CNVs are not part of structural variants.
C. non-CNV SVs can lead to the formation of multi-allelic CNVs.
D. Non-CNV structural variations involve changes in the structure of DNA but do not involve changes in copy number.
A and D
Which of the sequencing processes is useful for analyzing expressions of two genes that overlap
with each other on opposite strands?
A. Short read RNA sequencing
B. Long read RNA sequencing
C. Long read direct RNA sequencing
D. Strand specific RNA sequencing
E. Small RNA sequencing
D
Which of the statements is true about STAR?
A. STAR follows sequential seed searching.
B. In this process, the algorithm divides all reads into small fragments.
C. Reads are matched for maximum mappable prefix against the reference genome
sequence.
D. Seed searching requires building suffix tree from the reference genome.
A and C
Which of these algorithms follows the alignment-free method?
A. Kallisto
B. Salmon
C. HISAT2
D. Sailfish
E. TopHat
A B D
Which of the transcript quantification algorithm(s) use the Expectation-Maximization (EM)
algorithm or a similar probabilistic model for isoform quantification?
A. RSEM
B. Hash table
C. Kalisto
D. Burrows wheeler transform
A and C
Which of the following statements are true regarding the use of the BWT?
A. In the reference genome, alternative splicing events are managed by BWT.
B. The reference genome is compressed using BWT for effective storage.
C. Fast and memory-efficient alignment of sequencing reads is made possible by BWT.
D. Exact matches (seeds) between the read and the reference genome are found using BWT.
B C D
