an R package to detect and quantify ORF translation using Ribo-seq data
SaTAnn (Splice-aware Translatome Annotation) is an R package that aims at detecting and quantifiying ORF translation on complex transcriptomes using Ribo-seq data. This package uses syntax and functions present in Bioconductor packages like GenomicFeatures, rtracklayer or BSgenome. SaTAnn aims at quantifying translation at the single ORF level taking into account the presence of multiple transcripts expressed by each gene. To do so, the SaTAnn pipeline consists of transcript filtering, de-novo ORF finding, ORF quantification and ORF annotation. A variety of annotation methods, both in transcript and genomic space, is performed for each ORF, to yield a more complete picture of alternative splice sites usage, uORF translation, translation on NMD candidates etc... More details can be found in our manuscript:
SaTAnn quantifies translation on the functionally heterogeneous transcriptome
Lorenzo Calviello^, Antje Hirsekorn, Uwe Ohler^
biorXiv (2019), doi: https://doi.org/10.1101/608794
We recommend users to have a look at the vignette: https://htmlpreview.github.io/?https://github.com/lcalviell/SaTann/blob/master/SaTAnn_vignette.html, or our manual (SaTAnn_manual.pdf).
To install SaTAnn:
library("devtools") install_github(repo = "lcalviell/SaTAnn") library("SaTAnn")
Three steps are required to use SaTAnn on your data:
parses a .gtf and a .2bit file. (this need to be done once per each annotation-genome combination, a .2bit file can be obtained from a fasta file using the faToTwoBit software from UCSC: https://genome.ucsc.edu/goldenpath/help/twoBit.html - http://hgdownload.soe.ucsc.edu/admin/exe/ )
or (recommended) the Ribo-seQC package (https://github.com/lcalviell/Ribo-seQC) can create input files for SaTAnn using a Ribo-seq .bam file.
is the master function used to perform the entire analysis workflow, for single genes or (recommended) entire transcriptomes. Please check the vignette for an example workflow.
For any question, please email: