title: ST Pipeline: an automated pipeline for spatial mapping of unique transcripts.
abstract: BACKGROUND
  In recent years we have witnessed an increase in novel RNA-seq based techniques for transcriptomics analysis. Spatial transcriptomics is a novel RNA-seq based technique that allows spatial mapping of transcripts in tissue sections. The spatial resolution adds an extra level of complexity, which requires the development of new tools and algorithms for efficient and accurate data processing.
  
  
  RESULTS
  Here we present a pipeline to automatically and efficiently process RNA-seq data obtained from spatial transcriptomics experiments to generate datasets for downstream analysis.
  
  
  METHODS
  The ST Pipeline is open source under a MIT license and it is available at https://github.com/SpatialTranscriptomicsResearch/st_pipeline.
  
  
  BACKGROUND
  jose.fernandez.navarro@scilifelab.se.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
authors.forename: José Fernández
authors.initials: JF
authors.lastname: Navarro
authors.affiliation: Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
authors.forename: Joel
authors.initials: J
authors.lastname: Sjöstrand
authors.affiliation: Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Salmén
authors.affiliation: Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
authors.affiliation: Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Science for Life Laboratory, Solna, Sweden.|Department of Cell and Molecular Biology, SE-171 77 Karolinska Institutet, Stockholm, Sweden.
authors.forename: Patrik L
authors.initials: PL
authors.lastname: Ståhl
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D009928:Organ Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D062206:Spatial Analysis