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Vorlesung Bioinformatik





  1. blatt1.pdf (deutsch), sheet1.pdf (englisch), gene.train, gene.key,
  2. blatt2.pdf, sheet2.pdf, 2pois.sample
  3. blatt3.pdf, transcripts.fa, reads.fa, eXpress, bowtie2
    Tips: Go to the bowtie website and download the bowtie2 package (link to Bowtie2 2.2.2 on the right). You can download binary, e.g. 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 blatt3                 
    bowtie2 blatt3 --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 20 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.
  4. Übung 1 zum Micorarrays (keine Abgabe) Raumänderung:: Am 15.5., 22.5. und 5.6. findet die Übung im Labor für Zeitreihenanalyse statt. Das Labor befindet sich in der Franz-Mehring-Str. 48 im ersten Stock, erste Tür rechts.
  5. case studies
  6. Expressionsanalyse mit RNA-Seq, sheet6.pdf, counts.tbl.gz, factors.tbl,sheet6.R.template
    manual of the R-package edgeR
  7. blatt7.pdf
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