Befehlszeilentools für Tests zur Genomdatenwissenschaft & Antworten – Coursera

• Mehr
• gzip
• ls
• cp

• rmdir
• CD
• oben
• gzip

• Jahr
• 50
• 12
• Monate

• 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

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

”’

• cd apple
• rm *
• CD ../..
• mv apple plum

”’

• • /home/Coursera/L1/apple
  • /home/Coursera/L1/apple
  • /home/Coursera
  • /home/Coursera

• • L1
  • Coursera
  • Apfel
  • plum

• • plum
  • Apfel
  • pear
  • strawberry

• • /home/Coursera/L1
  • /home/Coursera/L1/apple
  • L1/apple
  • /home/Coursera/L1

• 4, 6
• 12, 20
• 5, 10
• 12, 12

• 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

• 3, 2, 2
• 5,2,3
• 3, 1, 3
• 2, 4, 5

• cat p/genes strawberry/genes | tail -1
• Kopf -1 p/genes strawberry/genes
• Weniger /G | Kopf -1
• cat p/genes strawberry/genes | grep –c 1

 

• APCTSYFPEITHI
• AAAAAAAAA
• AGCTACTACGAGCT
• CCCCCCCCCC

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

• 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.

• Soft clipping
• Cut and paste
• Hard clipping
• Padding

• 1
• 2
• 3
• 4

• 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

• Gene: 1; Transkripte: 2; Exons: 2,2; Strand: -; Length of 5’ exon(s): 2736, 2194.
• Gene: 1; Transkripte: 2; Exons: 2,2; Strand: -; Length of 5’ exon(s): 2735, 2193.
• Gene: 1; Transkripte: 1; Exons: 4; Strand: -; Length of 5’ exon(s): 2736.
• Gene: 1; Transkripte: 4; Exons: 1,1,1,1; Strand: -; Length of 5’ exon(s): 2736, 1417,2194,795.

• 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.

• 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.

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

 

• 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

• 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.

• samtools
• mkdir
• bcftools
• bedtools

• 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.

• –lokal
• -D
• –ignore-quals
• –empfindlich

• Only site 2 shows potential variation;

  the alternate letter for site 2 is ‘.’;

  Seite? ˅ 1 hat 8 supporting reads, and site 2 hat 16

• Only site 2 shows potential variation;

  the alternate letter for site 2 is G;

  Seite? ˅ 1 hat 8 supporting reads, and site 2 hat 16

• Only site 2 shows potential variation;

  the alternate letter for site 2 is A;

  Seite? ˅ 1 hat 8 supporting reads, and site 2 hat 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

• Average mapping quality for variant 3 ist 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

• 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, beziehungsweise;

• 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

• 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

• 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

• 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.

• 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

• cufflinks, bowtie
• tophat, Teilt
• tophat, bowtie
• tophat, cufflinks

• 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.

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

• 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.

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

• 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

• 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

• 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