- Illumina or Torrent run report
- Image Files (BCL)
- Raw/pooled FASTQ files
- FASTQC report
- Genome aligned reads (BAM) (Hisat2 Fast and sensitive spliced alignment (DOI:10.1038/nprot.2016.095) and Bowtie2 Ultrafast read alignment (DOI:10.1038/nmeth.1923)
- Visualization with BedGraph files uploaded to UCSC Genome Browser
- Read counts per gene (HTSeq doi:10.1093/bioinformatics/btu638)
- Differential expression analysis for RNA-seq with different algorithms/software:
- Fragments per Million of read (FPKM) Cufflinks: Isoform assembly and quantitation for RNA-Seq (PMID: 22383036)
- Reads per gene, count based algorithms edgeR (PMID: 19910308) and DESeq (PMID: 25516281), implemented in the MetaseqR (DOI:10.1093/nar/gku1273), and SARTools (PMID: 27280887)
- Table of results, graphs (pairwise scatter, cluster dendrogram, multi-dimensional scaling, raw & normalized distribution, volcano)
- For ChIP-seq, peak calling with macs2 (doi: 10.1186/gb-2008-9-9-r137) and downstream analysis with various tools
