This script performs all relevant preprocessing of DNA-seq data (currently with settings for ChIP-seq and ATAC-seq) starting with fastqc control, adapter trimming, alignment, filtering, peak calling, FRiP calculation, library complexity assessment, browser track creation, summary statistics/multiqc. THere are a few options that can be set in the header such as number of parallel jobs and presets for ATACseq and ChIPseq and the input format and layout (uBam or Fastq, paired- or single-end runs, but not mixed). Expects input files to be in same directory as the script itself.
Folder contains some scripts to analyze ATAC-seq data such as a wrapper to run chromVAR.
Same as ATAC-seq but for, guess what, ChIP-seq data.
Draft for a wrapper for the HiCUPs pipeline.
Wrappers for quantifications with salmon or hisat2. hisat2 script also contains some quality assessment via RSeqC.
Still, salmon is the preferred quantification pipeline as it respects multimappers and implements GC bias correction with the method implemented in the BioC package alpine plus is directly compatible with tximport to create depth/length offsets for use in edgeR.
Draft script for quantification of scRNA-seq reads per cell via alevin. Currently more orless untested and preliminary.
Folder contains wrapper scripts to run csaw (ATAC-seq/ChIP-seq), edgeR (RNA-seq) given tximport input, tximport to import transcript abundance estimated from salmon and some scripts to plot volcanos and MA-plots in a more or less automated/reproducible fashion.