Bioconductor-for-Genomic-Data-Science Quizzes & 答案 - Coursera

Exploring the depths of genomic data science has never been more accessible, thanks to platforms like Coursera. 该 ‘Bioconductor-对于-Genomic–数据–科学‘ course offers a comprehensive dive into the tools and techniques essential for today’s genomic research.

Before delving into the specifics of the 测验和答案, it’s crucial to understand the value this course brings to both novices and seasoned scientists in the field. This write-up aims to shed light on the pivotal concepts and methodologies you’ll encounter, paving your way to mastering genomic data science.

测验 1

第一季度. Use the AnnotationHub package to obtain data on “CpG Islands” in the human genome.

题: How many islands exists on the autosomes?

回答: 26641

Q2. How many CpG Islands exists on chromosome 4?

回答: 1031

Q3. Obtain the data for the H3K4me3 histone modification for the H1 cell line from Epigenomics Roadmap, using AnnotationHub. Subset these regions to only keep regions mapped to the autosomes (染色体 1 至 22).

题: How many bases does these regions cover?

回答: 41135164

第四季度. H3K27me3 histone modification for the H1 cell line from Epigenomics Roadmap

回答: 4.770728

Q5. Bivalent regions are bound by both H3K4me3 and H3K27me3

回答: 10289096

Q6. We will examine the extent to which bivalent regions overlap CpG Islands.

题: how big a fraction (expressed as a number between 0 和 1) of the bivalent regions, overlap one or more CpG Islands?

回答: 0.5383644

Q7. How big a fraction (expressed as a number between 0 和 1) of the bases which are part of CpG Islands, are also bivalent marked.

回答: 0.241688

Q8. How many bases are bivalently marked within 10kb of CpG Islands?

回答: 9782086

Q9. Fraction of CpG

回答: 0.007047481

辅酶Q10. Calculate odds ratio from contigency table

回答: 169.0962

测验 2

第一季度. What is the GC content of “chr22” in the “hg19” build of the human genome?

回答: 0.4798807

Q2. What is the mean GC content of H3K27me3 “narrowPeak” regions of Epigenomics Roadmap from the H1 stem cell line on chr 22.

回答: 0.528866

Q3. What is the correlation between GC content and “signalValue” of these regions (on chr22)?

回答: 0.004467924

第四季度. What is the correlation between the “signalValue” of the “narrowPeak” regions and the average “fc.signal” across the same regions?

回答: 0.9149614

Q5. How many bases on chr22 have an fc.signal greater than or equal to 1?

回答: 10914671

Q6. Identify the regions of the genome where the signal in E003 is 0.5 or lower and the signal in E055 is 2 或更高.

回答: 1869937

Q7. What is the average observed-to-expected ratio of CpG dinucleotides for CpG Islands on chromosome 22?

回答: 0.8340929

Q8. How many TATA boxes are there on chr 22 of build hg19 of the human genome?

回答: 27263

Q9. How many transcript promoters are on chromosome 22, which contain a coding sequence, such as a TATA box on the same strand as the transcript?

回答: 218

辅酶Q10. How many bases on chr22 are part of more than one promoter of a coding sequence?

回答: 309991

测验 3

第一季度. What is the mean expression across all features for sample 5 in the ALL dataset(from the ALL package)?

回答: 5.629627

Q2. Using the Ensembl 75, annotate each feature of the ALL dataset with the Ensembl gene id. How many probesets (特征) are annotated with more than one Ensembl gene ID?

回答: 1045

Q3. How many probesets (Affymetrix IDs) are annotated with one or more genes on the autosomes (chr 1-22)

回答: 11016

第四季度. What is the mean value of the Methylation channel across the features for sample #”5723646052_R04C01″

回答: 7228.277

Q5. Access the processed data from NCBI GEO Accession number GSE788, what is the mean expression level of sample GSM9024?

回答: 756.432

Q6. What is the average of the average length across the samples in the expriment?

回答: 113.75

Q7. What is the number of Ensembl genes which have a count of 1 read or more in sample SRR1039512?

回答: 25699

Q8. The airway dataset contains more than 64k features. How many of these features overlaps with transcripts on the autosomes (染色体 1-22) as represented by the TxDb.Hsapiens.UCSC.hg19.knownGene package?

回答: 26276

Q9. The expression measures of the airway dataset are the number of reads mapping to each feature.

回答: 0.853774

辅酶Q10. What is the median number of counts per feature (for sample SRR1039508) containing a H3K4me3 narrowPeak in their promoter (only features which overlap autosomal transcripts from TxDb.Hsapiens.UCSC.hg19.knownGene are considered)?

回答: 232

测验 4

第一季度. What fraction of reads in this file has an A nucleotide in the 5th base of the read?

回答: 0.3638

Q2. What is the average numeric quality value of these reads?

回答: 28.93

Q3. In this interval, how many reads are dupicated by position?

回答: 129.00

第四季度. What is the average number of reads across the 8 samples falling in this interval?

回答: 90.25

Q5. What is the average expression across samples in the control group for the “8149273” probeset (this is a character identifier, not a row number)

回答: 7.0218

Q6. What is the absolute value of the log foldchange(logFC) of the gene with the lowest P.value?

回答: 0.7126

Q7. How many genes are differentially expressed between the two groups at an adj.P.value cutoff of 0.05

回答: 0

Q8. What is the mean difference in beta values between the 3 normal samples and the 3 cancer samples,across OpenSea CpG?

回答: 0.0846

Q9. How many of these DNase hypersensitive sites contain one or more CpG on the 450k array?

回答: 40151

辅酶Q10. How many features are differentially expressed between control and treatment (ie.padj <= 0.05)?

回答: 87

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Bioconductor-for-Genomic-Data-Science Quizzes & 答案 – Coursera