Code for calling resource intensive functions of Sierra.
Dependencies are:
optparse(CRAN)devtools(CRAN)Sierra(github)
Install them like so:
install.packages(c("optparse", "devtools"))
devtools::install_github("VCCRI/Sierra", build = TRUE)
docker pull geertvangeest/sierra:latestsingularity pull docker:https://geertvangeest/sierra:latestThe functions FindPeaks, CountPeaks, MergePeakCoordinates and AnnotatePeaksFromGTF are incorporated in a shell script and callable from the command line. You find them in the directory scripts. Get usage info by typing Rscript [function].R -h.
E.g. Rscript AnnotatePeaksFromGTF.R -h results in:
Usage: ./scripts/AnnotatePeaksFromGTF.R [options]
Annotate a set of peak coordinates according to genomic features the coordinates fall on - 3'UTR, exon, intron and 5'UTR, and annotate proximity to motifs. Motifs include the canonical polyA motif, A-rich regions and T-rich regions.
Options:
-p PEAKS_SITES_FILE, --peaks_sites_file=PEAKS_SITES_FILE
a file of peak coordinates.
-g GTF_FILE, --gtf_file=GTF_FILE
GTF reference file.
-o OUTPUT_FILE, --output_file=OUTPUT_FILE
file to write the annotations to [default = peak_annotations.txt]
-r GENOME, --genome=GENOME
BSGenome package (e.g. BSgenome.Mmusculus.UCSC.mm10). Will be installed if not available
-l LIBRARY, --library=LIBRARY
Path in which to install BSGenome package (should be writeable)
-h, --help
Show this help message and exit
For example for AnnotatePeaksFromGTF.R:
docker run --rm geertvangeest/sierra AnnotatePeaksFromGTF.R -hFor example for AnnotatePeaksFromGTF.R:
./sierra_latest.sif AnnotatePeaksFromGTF.R -hor
singularity exec ./sierra_latest.sif AnnotatePeaksFromGTF.R -h