Dependencies

This page lists software dependencies for the tutorials. This is useful for people without access to HPC Rackham on Uppmax.

ChIP-seq

Requirements for ChIP-seq labs.

Software	Version	Lab	Comment
samtools	0.1.19 & 1.18	processing and QC	both versions
phantompeakqualtools	1.2 (*)	processing and QC	https://github.com/kundajelab/phantompeakqualtools
Picard	2.23.4	processing and QC
NGSUtils	0.5.9	processing and QC
deepTools	3.3.2	processing and QC; visualisation
MACS	2.2.6	peak calling
BEDTools	2.29.2	peak calling
BEDOPS	2.4.3	peak calling
epic2	0.0.52 (**)	broad peaks	https://github.com/biocore-ntnu/epic2
csaw	1.24.3	broad peaks

In addition, the following Bioconductor libraries are used in the tutorials:

• annotation: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene,``reactome.db``,``biomaRt``

• analysis: DiffBind, edgeR, ChIPQC ``, ``ChIPpeakAnno,``ChIPseeker``,``ReactomePA``,``clusterProfiler``

(*) You will notice that we use a conda environment for phantompeakqualtools, along with two versions of of samtools loaded as modules. This is because we have encountered incompatibilities with how phantompeakqualtools saves temporary data and recent versions of R, and also syntax differences between samtools versions and libraries required for processing bam files produced by newer samtools versions. Long story short, while a bit clunky, this solution works on our system.

Conda environment was produced using:

module load conda/latest

conda create --prefix /path/to/your/environments/xcor -c bioconda phantompeakqualtools=1.2.1.1

(**) Newer versions of Pysam seem to throw errors when used with epic2. We have tested the configuration below and it works on our system.

Conda environment was produced using:

module load conda/latest

conda create --prefix /path/to/your/environments/epic_2b -c conda-forge python=3.7

pip install Cython
pip install pysam==0.15.2
pip3 install epic2

ATAC-seq

Requirements for ATAC-seq labs.

Software	Version	Lab	Comment
samtools	1.18

Methylation

Requirements for both methylation labs (all of these are R packages).

Software	Version
R	4.0.0
limma	3.44.3
minfi	1.34.0
RColorBrewer	1.1-2
missMethyl	1.22.0
minfiData	0.34.0
Gviz	1.32.0
DMRcate	2.2.3
DMRcatedata	2.10.0
stringr	1.4.0
mCSEA	1.12.0
methylKit	1.14.2
genomation	1.20.0
GenomicRanges	1.40.0