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Vorlesung Bioinformatik

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Vorlesung

Übungen

  1. blatt1.pdf, gene.train, gene.key
  2. blatt2.pdf, 2pois.sample
  3. blatt3.pdf, dss.train.txt, dss.test.pos.txt, dss.test.neg.txt,
  4. blatt4.pdf, abweichende Abgabefrist: Aufgabe 2 ist erst am 14. Mai fällig
  5. blatt5.pdf
  6. blatt6.pdf
  7. blatt7.pdf
  8. blatt8.pdf
  9. blatt9.pdf
  10. blatt10.pdf, dss1.txt, dss2.txt, dss3.txt
  11. blatt11.pdf, transcripts.fa, reads.fa
    Tipps: Go to the bowtie website and download the bowtie2 package (link to Bowtie2 2.1.0 on the right). You can download binary, e.g. bowtie2-2.1.0-linux-x86_64.zip or whatever matches your machine type. You will need the two executables bowtie2 and bowtie2-build, the later to build an index for fast mapping.
    Go to the eXpress homepage and download the current version. Then build the index, align the reads and quantify by running
    bowtie2-build transcripts.fa blatt11
    bowtie2 blatt11 --rdg 100,100 --rfg 100,100 -k 4 -f -U reads.fa > hits.sam
    express --no-error-model --no-bias-correct -m 20 -s 1 -B 1 transcripts.fa hits.sam
    
    The options to bowtie2 make indels so expensive that alignments with gaps are not reported. At most 4 alignments per read are reported.
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