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Introduction to RNA-seq and ChIP-seq data analysis using PAF1 Cell 2015 article
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RNA-seq and ChIP-seq data analysis: Course Material

Data and session setup

Data presentation

Session setup

Sequences, annotations and indexes

  • Genome sequence (fasta)
  • Annotations (GTF file):
  • STAR index
  • Bowtie2 index
  • Transcripts sequences

Raw data (reads)


RNA-seq

Raw reads - QC - Trimming

  • QC
  • Trimming

Alignment

Counting and differential expression analysis

Estimates of expression levels

Signal files for genome browser


ChIP-seq

Raw reads - QC - Trimming

Alignment

Signal files

Peak calling

Peak annotation

Heatmaps and average profiles

Sequences for motif search


References

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