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

Exploring the depths of genomic data science has never been more accessible, thanks to platforms like Coursera. Il ‘Bioconductor-per-Genomico–Dati–Scienza‘ course offers a comprehensive dive into the tools and techniques essential for today’s genomic research.

Before delving into the specifics of the quiz e risposte, 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.

Quiz 1

Q1. Use the AnnotationHub package to obtain data on “CpG Islands” in the human genome.

Domanda: How many islands exists on the autosomes?

Q2. How many CpG Islands exists on chromosome 4?

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 (cromosomi 1 a 22).

Domanda: How many bases does these regions cover?

Q4. H3K27me3 histone modification for the H1 cell line from Epigenomics Roadmap

Q5. Bivalent regions are bound by both H3K4me3 and H3K27me3

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

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

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

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

D9. Fraction of CpG

Q10. Calculate odds ratio from contigency table

Quiz 2

Q1. What is the GC content of “chr22” in the “hg19” build of the human genome?

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

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

Q4. What is the correlation between the “signalValue” of the “narrowPeak” regions and the average “fc.signal” across the same regions?

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

Q6. Identify the regions of the genome where the signal in E003 is 0.5 or lower and the signal in E055 is 2 o più alto.

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

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

D9. 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?

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

Quiz 3

Q1. What is the mean expression across all features for sample 5 in the ALL dataset(from the ALL package)?

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

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

Q4. What is the mean value of the Methylation channel across the features for sample #”5723646052_R04C01″

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

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

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

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

D9. The expression measures of the airway dataset are the number of reads mapping to each feature.

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)?

Quiz 4

Q1. What fraction of reads in this file has an A nucleotide in the 5th base of the read?

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

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

Q4. What is the average number of reads across the 8 samples falling in this interval?

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)

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

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

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

D9. How many of these DNase hypersensitive sites contain one or more CpG on the 450k array?

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