Introduction

The tximeta package (Love et al. 2019) extends the tximport package (Soneson, Love, and Robinson 2015) for import of transcript-level quantification data into R/Bioconductor. It automatically adds annotation metadata when the RNA-seq data has been quantified with Salmon (Patro et al. 2017) or for scRNA-seq data quantified with alevin (Srivastava et al. 2019). To our knowledge, tximeta is the only package for RNA-seq data import that can automatically identify and attach transcriptome metadata based on the unique sequence of the reference transcripts. For more details on these packages – including the motivation for tximeta and description of similar work – consult the References below.

Note: tximeta requires that the entire output directory of Salmon / alevin is present and unmodified in order to identify the provenance of the reference transcripts. In general, it’s a good idea to not modify or re-arrange the output directory of bioinformatic software as other downstream software rely on and assume a consistent directory structure. For sharing multiple samples, one can use, for example, tar -czf to bundle up a set of Salmon output directories, or to bundle one alevin output directory. For tips on using tximeta with other quantifiers see the other quantifiers section below.