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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