A STAR RNA-seq Log.final.out report shows: Uniquely mapped r…

A STAR RNA-seq Log.final.out report shows: Uniquely mapped reads % = 42%, Unmapped (too short) % = 35%, Multi-mapping % = 3%. What is the most likely interpretation and appropriate first troubleshooting step? A) This is excellent-quality data requiring no further action B) The low unique-mapping rate combined with a high “too short” unmapped percentage suggests possible adapter contamination or an incorrect/mismatched reference genome; the appropriate first step is to re-check FastQC adapter content and confirm the correct reference/species were used C) The high multi-mapping rate is the primary cause of the poor result D) The library was simply over-sequenced and should be down-sampled

A researcher sequences 5,000 individual cells from a single…

A researcher sequences 5,000 individual cells from a single mouse and treats each cell as an independent biological replicate (n = 5,000) in a differential expression comparison. What statistical error does this represent? A) A batch effect B) A multiple-testing error C) Pseudoreplication D) A Type II error

A SAM alignment record has FLAG = 99. Using standard bitwise…

A SAM alignment record has FLAG = 99. Using standard bitwise FLAG decoding (1 = paired, 2 = proper pair, 32 = mate reverse strand, 64 = first in pair), what does this FLAG indicate? A) The read is unmapped B) This is a properly paired, first-in-pair (Read 1) alignment whose mate is on the reverse strand C) The read is a PCR duplicate D) The read is a secondary alignment

What is the key structural difference between a standard VCF…

What is the key structural difference between a standard VCF file and a GVCF file? A) GVCF stores only SNPs, while VCF stores only indels B) GVCF contains a record for every genomic position, including non-variant reference blocks, while standard VCF reports only variant positions C) VCF is a binary format while GVCF is plain text D) GVCF cannot be used for downstream joint genotyping

BED and GTF are both genomic interval formats, but their coo…

BED and GTF are both genomic interval formats, but their coordinate systems differ. Which statement is correct? A) Both formats use 1-based, closed coordinates B) BED uses 0-based, half-open coordinates; GTF uses 1-based, closed coordinates C) BED uses 1-based coordinates; GTF uses 0-based coordinates D) Both formats use 0-based, half-open coordinates