Skip to content
an R package to detect and quantify ORF translation using Ribo-seq data
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
inst/rmd Update SaTAnn_template.Rmd Apr 13, 2019
man
.Rbuildignore
.Rhistory
.gitignore upload files Apr 13, 2019
DESCRIPTION
NAMESPACE
README.md
SaTAnn-manual.pdf
SaTAnn.Rproj
SaTAnn_0.99.0.tar.gz
SaTAnn_0.99.0_paper_version.tar.gz
SaTAnn_vignette.Rmd
SaTAnn_vignette.html

README.md

SaTAnn

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

https://www.biorxiv.org/content/10.1101/608794v1

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:

?prepare_annotation_files

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/ )

?prepare_for_SaTAnn

or (recommended) the Ribo-seQC package (https://github.com/lcalviell/Ribo-seQC) can create input files for SaTAnn using a Ribo-seq .bam file.

?run_SaTAnn

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:

calviello.l.bio@gmail.com or uwe.ohler@mdc-berlin.de

Enjoy!

You can’t perform that action at this time.