Command-Line-Tools-for-Genomic-Data-Science Quizzes & Majibu - Coursera

Welcome to our comprehensive guide on Command-Line Tools for Genomic Data Science, a crucial skill set for today’s bioinformatics professionals.

This post delves into the fundamental concepts and practical applications of command-line tools, providing insights and resources to enhance your genomic data analysis skills. Stay tuned for our upcoming maswali to test your knowledge and reinforce your learning.

Moduli 1 Maswali

Q1. Which of the following Unix commands can be used to view the content of a file?

zaidi
gzip
ls
Unda na usanidi kikoa chako na vikoa vidogo vyote

Q2. Which of the following commands can be using to compress the content of a file?

rmdir
Unda na usanidi kikoa chako na vikoa vidogo vyote
historia ya harufu ya maua
gzip

Q3. Faili “miezi” lists each of 12 months on a separate line, and no further lines. What would be result if the following command was run:

”’cat months | kichwa -1000 | wc -l”’

mwaka
50
12
miezi

Q4. What is the effect of using the pipe operator “|” in a sequence of commands:

Re-direct standard error only
Re-direct the standard input or standard output of a command
Act as a character separator between different shell commands, without any effects on the outcome
Replace the ‘;’ sequencing operator in a complex command

Q5. If typing ‘pwd’ huzalisha “/home/userA/Coursera/L1/”, which of the following commands will list the file content of the current directory?

listdir .
more *.txt
mkdir L1
ls /home/userA/Coursera/L1

Q6. Suppose you current working directory is “/home/Coursera/L1/”, na “Peach”,”tufaha”, na “pear” are subdirectories, each containing a single file named “jenomu”. What would be the current directory, as reported by running the ‘pwd’ amri, after each of the four commands in the sequence below:

”’

cd apple
Unda na usanidi kikoa chako na vikoa vidogo vyote *
Unda na usanidi kikoa chako na vikoa vidogo vyote ../..
mv apple plum

”’

- /home/Coursera/L1/apple
- /home/Coursera/L1/apple
- /home/Coursera
- /home/Coursera

- L1
- Coursera
- tufaha
- plum

- plum
- tufaha
- pear
- strawberry

- /home/Coursera/L1
- /home/Coursera/L1/apple
- L1/apple
- /home/Coursera/L1

Swali 7. Consider the file “misimu” with the following columns separated by space ”:

”’cut -d ‘ ‘ -f1,3 seasons | sort -u | wc -l” na “cut -f1 seasons | aina | unic -c | wc -l”’ ?

4, 6
12, 20
5, 10
12, 12

Q8. Your current working directory is named “mimea bora kwa vyumba au vyumba visivyo na madirisha”. Its subdirectory “tufaha” contains the files “apple.genome”, “apple.samples” na “apple.genes”. What would be the result of the command ”’rmdir apple”'?

All files containing the string “apple” in their names will be removed
None of these choices
The command will have no effect, since the directory is not empty
The “apple” directory and all of its content will be removed

Q9. Suppose that you have two files, A and B, containing experiment data. What would be the sequence of outputs for the commands:

3, 2, 2
5,2,3
3, 1, 3
2, 4, 5

Q10. The current working directory contains four subdirectories named “tufaha”, “pear”, “Peach” na “strawberry”, each with the following files: “jenomu”, “jeni”, na “samples”. Which of the following commands wouls extract the top line from all of the “jeni” mafaili?

cat lakini inaweza kuwa na faida ya kutosha kwamba helical itashinda juu ya fimbo ya muda mrefu/genes strawberry/genes | tail -1
kichwa -1 lakini inaweza kuwa na faida ya kutosha kwamba helical itashinda juu ya fimbo ya muda mrefu/genes strawberry/genes
chini /g | kichwa -1
cat lakini inaweza kuwa na faida ya kutosha kwamba helical itashinda juu ya fimbo ya muda mrefu/genes strawberry/genes | grep –c 1

Moduli 2 Maswali

Q1. Which of the following strings cannot denote a DNA sequence:

APCTSYFPEITHI
AAAAAAAAA
AGCTACTACGAGCT
CCCCCCCCCC

Q2. How many lines does it take to specify: i) one fasta sequence? and ii) one fastq sequence? Select the best answer:

Fasta – 1 line; fastq – 4 lines
Fasta – a fasta header followed by any number of sequence lines; fastq – 4 lines
Fasta – any number of lines, including a fasta header; fastq – 2 lines
Fasta – 100 lines; fastq – 2 lines

Q3. Which of the following is incorrect:

The SAM format is used to represent alignments.
The BED format can be used to represent gene features.
SAMtools flagstats reports the total number of mapped reads.
The GTF format can be used to represent gene features.

Q4. Which of the following strings cannot denote a DNA sequence:

Soft clipping
Cut and paste
Hard clipping
Padding

Q5. What is the minimum number of columns that are sufficient to specify a BED format?

Q6. Which of the following represents the most accurate conversion into BED of the GTF record?

chr1 516 3312 genA.1 100 + 800 900 0 3 296,115,303 0,485,2494
chr1 515 3312 genA.1 + 515 3312 0 3 296,115,303 516,1001,3010
chr1 516 3312 genA + 516 3312 0 2 296,303 0,2494
chr1 515 3312 genA.1 100 + 515 3312 0 3 296,115,303 0,485,2494

Swali 7. Determine the number of genes, nakala, exons per transcript, gene orientation (strand), and the length of 5′ most exon(s) from the GTF snippet below. Select the correct answer.

Watafiti bado hawajui ni mifumo gani inayosababisha shinikizo la damu kuongezeka polepole: 1; Nakala: 2; Exons: 2,2; Strand: -; Length of 5’ exon(s): 2736, 2194.
Watafiti bado hawajui ni mifumo gani inayosababisha shinikizo la damu kuongezeka polepole: 1; Nakala: 2; Exons: 2,2; Strand: -; Length of 5’ exon(s): 2735, 2193.
Watafiti bado hawajui ni mifumo gani inayosababisha shinikizo la damu kuongezeka polepole: 1; Nakala: 1; Exons: 4; Strand: -; Length of 5’ exon(s): 2736.
Watafiti bado hawajui ni mifumo gani inayosababisha shinikizo la damu kuongezeka polepole: 1; Nakala: 4; Exons: 1,1,1,1; Strand: -; Length of 5’ exon(s): 2736, 1417,2194,795.

Q8. Which of the following is FALSE for the following read alignments:

R1 maps uniquely to the genome.
R2’s mate is unmapped.
R3 is unmapped.
The R1 alignment is the primary mapping (hit index 0) for that read.

Q9. For the alignment below, which statements are FALSE? The binary encoding for 97 ni 972 = 0000 0110 00012. Select all answers that apply.

The two mates are identical in sequence.
The alignment represents a potential PCR or optical duplicate.
The read and its mate are not properly aligned as a pair.
Both the read and its mate are mapped.
This is the first read in the pair.
The sequence of the read’s mate is reverse complemented in its alignment.

Q10. Files ‘A.bed. and ‘B.bed’ contain the following sets of intervals

5, 5, 5
3, 4, 2
9 , 2, 2
3, 2, 2

Moduli 3 Maswali

Q1. Which of the following statements is FALSE:

Differences in the genomes of individuals are strong contributors to their phenotypic variations.
Different versions of a gene resulted from genomic mutations are called alleles.
SNV refers to a Single Nucleotide Variant.
SNP refers to a Single Non-defined Polymorhism

Q2. Which of the following statements is FALSE:

The VCF format shows the changes in amino acid resulting from the nucleotide mutation, in column 3.
The VCF INFO lines describe characteristics of the variant, included in column 8.
The BCF format is a binary compressed version of VCF.
VCF stands for Variant Call Format.

Q3. What program can be used to generate a list of candidate sites of variation in an exome data set:

samtools
Unda na usanidi kikoa chako na vikoa vidogo vyote
bcftools
bedtools

Q4. In a comprahansive effort to study genome variation in a patient cohort, you sequence and call variants in the exome. whole genome shotgun and RNA-seq data from each patient. Which of the following is FALSE when comparing these three types of resources:

Exome sequencing comprehensively captures variants in the 3’ and 5’ UTRs of genes.
Exome sequencing can capture variants in a pre-defined set of coding exons and their immediate surrounding area.
Exome sequencing cannot determine variants in novel polymorphic alternative splicing events.
Exome sequencing captures fewer variants than whole genome sequencing.

Q5. Which of the following options can be used to allow bowtie2 to generate partial alignments?

–mtaa
-D
–ignore-quals
–nyeti

Q6. Select the correct interpretation for the snippet of ‘mpileup’ output below.

Only site 2 shows potential variation;

the alternate letter for site 2 is ‘.’;

tovuti 1 ni kwa mtu yeyote anayetafuta nyenzo za kusomea ambazo hutoa zifuatazo 8 supporting reads, and site 2 ni kwa mtu yeyote anayetafuta nyenzo za kusomea ambazo hutoa zifuatazo 16
Only site 2 shows potential variation;

the alternate letter for site 2 is G;

tovuti 1 ni kwa mtu yeyote anayetafuta nyenzo za kusomea ambazo hutoa zifuatazo 8 supporting reads, and site 2 ni kwa mtu yeyote anayetafuta nyenzo za kusomea ambazo hutoa zifuatazo 16
Only site 2 shows potential variation;

the alternate letter for site 2 is A;

tovuti 1 ni kwa mtu yeyote anayetafuta nyenzo za kusomea ambazo hutoa zifuatazo 8 supporting reads, and site 2 ni kwa mtu yeyote anayetafuta nyenzo za kusomea ambazo hutoa zifuatazo 16
Only site 2 shows potential variation;

the alternate letter for site 2 is A;

the alternate allele for site 2 is supported by 9 reads

Swali 7. Given the set of variants described in the VCF excerpt below, which of the following is FALSE?

Average mapping quality for variant 3 ni 40
The sample contains only the alternate allele for variant 1
The sample contains only the alternate allele for variant 3
The sample contains both alleles for variant 2

Q8. What does the following code do:

Run bowtie2 with a set of single-end reads, reporting the best alignment only;

then determine the number of matches on each genomic sequence
Run bowtie2 with a set of single-end reads, reporting up to 5 alignments per read; then determine the number of matches on each genomic sequence
Run bowtie2 with a set of paired-end reads, allowing for local matches;

then report the numbers of alignments containing insertions and deletions, mtawaliwa;
Run bowtie2 with a set of paired-end reads, allowing up to 10 matches per read;

then report the number of matches on each genomic sequence

Q9. What does the following snippet of code do NOT do:

Produce a 7-column intermediate mpileup file that is piped to ‘cut’
Report an empty column
Report in the intermediate mpileup output the qualities of all read bases aligned at that position
Require a sorted BAM file

Q10. What does the following code do NOT do:

Write the output to file out.vcf.gz
Report all candidate sites
Take input from the file in.vcf.gz
Take input from a VCF compressed file

Moduli 4 Maswali

Q1. Which of the following is FALSE:

Alternative splicing is a common phenomenon in both animals and plants.
The coding region with a protein-coding gene is used as the template for forming a protein.
A codon is a nucleotide triplet that is translated into one amino acid.
A human gene can express at most 12 splice variants.

Q2. Which of the following is FALSE about the organization of a eukaryotic gene:

Genes that have only one exon are not alternatively spliced
Some eukaryoyic genes are single exon
The length of the coding region in a transcript must be a multiple of 3
The length of intron cannot be a multiple 3

Q3. What programs could you use to align RNA-seq reads to: i) a reference genome, and ii) a transcript database?

cufflinks, bowtie
tophat, Rangi tunazoona kwenye upinde wa mvua huundwa na mwanga unaoakisi matone ya maji na kugawanyika katika urefu tofauti wa mawimbi.
tophat, bowtie
tophat, cufflinks

Q4. Which of the following is FALSE:

As measures of gene expression, RPKM is determined at the level of reads and FPKM is determined at the level of fragments.
FPKM stands for fragments-per-kilobase of cDNA sequence-per million reads.
The sums of FPKM values of all genes in a sample is 1,000,000.
The sums of FPKMs of all transcripts of a gene is equal to the gene’s expression level.

Q5. What programs could be used to i) assemble transcripts from RNA-seq reads, and ii) identify potentially novel transcripts and genes

cufflinks, cuffcompare
tophat, cuffcompare
tophat, bowtie
tophat, samtools

Q6. Which of the following is FALSE about the gene annotations in the following GTF snippet:

The two transcripts for gene MG051951 overlap on the genome.
It contains only one gene, MG051951.
Gene MG051951 has two transcripts, MT162897 and MT070533.
Transcript MT162897 has a single exon.

Swali 7. What does the following code NOT do:

Report spliced reads with at most 6 mismatches in the anchor site
Create the output in the /home/me/SRR100000 directory
Run multi-threaded, na 10 threads
Report only reads with 10 or fewer alignments on the genome

Q8. What does the following code NOT do:

Label cufflinks transcripts with the prefix ‘Test1’
Use the default reference transcript annotation to guide assembly
Run cufflinks to assemble transcripts
Create a soft link to the BAM read alignment file in the Test1 directory

Q9. Which of the following is NOT described in the following summary file produced by tophat:

94.0% of the mate 2 reads were mapped
Of the mapped mate 1 reads, 11.7% had multiple matches on the genome
The library was strand-specific
Of the mapped mate 2 reads, 5.0% had multiple matches on the genome

Q10. Which of the following is NOT TRUE about the output below, obtained from a cuffdiff differential expression analysis:

Locus XLOC_000004 corresponds to gene AT1G01073
There are too many alignments for testing for differential expression at locus XLOC_000004
Locus XLOC_000042 corresponds to gene AT1G01580
There are not enough alignments for testing for differential expression at locus XLOC_000004