Bioconductor-for-Genomic-Data-Science Quizzes & الأجوبة – كورسيرا
Exploring the depths of genomic data science has never been more accessible, thanks to platforms like Coursera. ال ‘Bioconductor-إلى عن على-Genomic–البيانات–علم‘ course offers a comprehensive dive into the tools and techniques essential for today’s genomic research.
Before delving into the specifics of the الإختبارات و الإجابات, 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.
لغز 1
Q1. Use the AnnotationHub package to obtain data on “CpG Islands” in the human genome.
سؤال: How many islands exists on the autosomes?
إجابه: 26641
Q2. How many CpG Islands exists on chromosome 4?
إجابه: 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 (الكروموسومات 1 إلى 22).
سؤال: How many bases does these regions cover?
إجابه: 41135164
Q4. H3K27me3 histone modification for the H1 cell line from Epigenomics Roadmap
إجابه: 4.770728
Q5. Bivalent regions are bound by both H3K4me3 and H3K27me3
إجابه: 10289096
Q6. We will examine the extent to which bivalent regions overlap CpG Islands.
سؤال: how big a fraction (expressed as a number between 0 و 1) of the bivalent regions, overlap one or more CpG Islands?
إجابه: 0.5383644
Q7. How big a fraction (expressed as a number between 0 و 1) of the bases which are part of CpG Islands, are also bivalent marked.
إجابه: 0.241688
Q8. How many bases are bivalently marked within 10kb of CpG Islands?
إجابه: 9782086
Q9. Fraction of CpG
إجابه: 0.007047481
Q10. Calculate odds ratio from contigency table
إجابه: 169.0962
لغز 2
Q1. What is the GC content of “chr22” in the “hg19” build of the human genome?
إجابه: 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.
إجابه: 0.528866
Q3. What is the correlation between GC content and “signalValue” of these regions (on chr22)?
إجابه: 0.004467924
Q4. What is the correlation between the “signalValue” of the “narrowPeak” regions and the average “fc.signal” across the same regions?
إجابه: 0.9149614
Q5. How many bases on chr22 have an fc.signal greater than or equal to 1?
إجابه: 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 أو أعلى.
إجابه: 1869937
Q7. What is the average observed-to-expected ratio of CpG dinucleotides for CpG Islands on chromosome 22?
إجابه: 0.8340929
Q8. How many TATA boxes are there on chr 22 of build hg19 of the human genome?
إجابه: 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?
إجابه: 218
Q10. How many bases on chr22 are part of more than one promoter of a coding sequence?
إجابه: 309991
لغز 3
Q1. What is the mean expression across all features for sample 5 in the ALL dataset(from the ALL package)?
إجابه: 5.629627
Q2. Using the Ensembl 75, annotate each feature of the ALL dataset with the Ensembl gene id. How many probesets (الميزات) are annotated with more than one Ensembl gene ID?
إجابه: 1045
Q3. How many probesets (Affymetrix IDs) are annotated with one or more genes on the autosomes (chr 1-22)
إجابه: 11016
Q4. What is the mean value of the Methylation channel across the features for sample #”5723646052_R04C01″
إجابه: 7228.277
Q5. Access the processed data from NCBI GEO Accession number GSE788, what is the mean expression level of sample GSM9024?
إجابه: 756.432
Q6. What is the average of the average length across the samples in the expriment?
إجابه: 113.75
Q7. What is the number of Ensembl genes which have a count of 1 read or more in sample SRR1039512?
إجابه: 25699
Q8. The airway dataset contains more than 64k features. How many of these features overlaps with transcripts on the autosomes (الكروموسومات 1-22) as represented by the TxDb.Hsapiens.UCSC.hg19.knownGene package?
إجابه: 26276
Q9. The expression measures of the airway dataset are the number of reads mapping to each feature.
إجابه: 0.853774
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)?
إجابه: 232
لغز 4
Q1. What fraction of reads in this file has an A nucleotide in the 5th base of the read?
إجابه: 0.3638
Q2. What is the average numeric quality value of these reads?
إجابه: 28.93
Q3. In this interval, how many reads are dupicated by position?
إجابه: 129.00
Q4. What is the average number of reads across the 8 samples falling in this interval?
إجابه: 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)
إجابه: 7.0218
Q6. What is the absolute value of the log foldchange(logFC) of the gene with the lowest P.value?
إجابه: 0.7126
Q7. How many genes are differentially expressed between the two groups at an adj.P.value cutoff of 0.05
إجابه: 0
Q8. What is the mean difference in beta values between the 3 normal samples and the 3 cancer samples,across OpenSea CpG?
إجابه: 0.0846
Q9. How many of these DNase hypersensitive sites contain one or more CpG on the 450k array?
إجابه: 40151
Q10. How many features are differentially expressed between control and treatment (ie.padj <= 0.05)?
إجابه: 87
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