Minimum Dependencies RNA/ATAC:
- Trimmomatic 0.39: http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
- STAR 2.6.1d: https://github.com/alexdobin/STAR
- DESeq2 1.18.1: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
- Picard 2.21.7: https://github.com/broadinstitute/picard
- SubRead featureCounts 1.6.4: https://subread.sourceforge.net/
- Samtools 1.15: https://github.com/samtools/samtools
- Deeptools bamCoverage 3.5.1: https://github.com/deeptools/deepTools
- Encode tools v2: https://www.encodeproject.org/software/bigwigaverageoverbed/
Dependencies ATAC specific:
- Macs3 3.0.0a7: https://github.com/macs3-project/MACS
Tested with:
- OS Debian 11 bullseye https://www.debian.org/releases/ and https://www.debian.org/releases/bullseye/installmanual
Install dependencies listed above according to respective manuals.
Typical install time is 5 hours, depending on the experience level of the user.