Program Dependencies

Transcriptomics (RNA-Seq)

• fastqc
• trimmomatic
• STAR
• samtools
• featureCounts (subread)
• deepTools
• R (with DESeq2, ggplot2, etc.)

Chromatin Accessibility (ATAC-Seq)

• fastqc
• fastp
• bowtie2
• samtools
• picard
• macs2
• deepTools
• bedtools

Protein-DNA Interaction (ChIP-Seq, CUT&RUN, CUT&Tag)

• fastqc
• fastp
• bowtie2
• samtools
• picard
• macs2
• deepTools
• bedtools