Read a STARsolo splice-junction (SJ) matrix

Loads the per-cell splice-junction count matrix produced by STARsolo with --soloFeatures SJ and relabels its junctions into the chr-start-end-strand ID form Matisse expects for junction mode (the first pattern recognised by the internal junction-ID parser, so the counts are ready for CreateMatisseObject and sashimi plots).

Usage

ReadSTARsoloSJ(
  sj_dir,
  cells = NULL,
  strand_map = c(`0` = "*", `1` = "+", `2` = "-"),
  infer_strand = TRUE,
  verbose = TRUE
)

Arguments

sj_dir

Directory holding matrix.mtx, barcodes.tsv and features.tsv (optionally .gz). Typically a STARsolo Solo.out/SJ/raw directory.

cells

Optional character vector of cell barcodes to keep (e.g. colnames(seurat)). Barcodes absent from the SJ matrix are dropped with a warning. Default: NULL (keep all).

strand_map

Named character vector mapping STAR strand codes to symbols. Default: c("0" = "*", "1" = "+", "2" = "-").

infer_strand

Logical. When the STAR strand code is 0 (undefined) but the intron-motif column is canonical, recover the strand from the motif (1/3/5 -> +, 2/4/6 -> -; 0 stays undefined). Roughly one in six STARsolo junctions are strand-undefined; without this they can never match the +/- junction IDs in a SUPPA2 event table. Default: TRUE.

verbose

Logical. Print progress. Default: TRUE.

Value

A dgCMatrix of raw junction counts, cells x junctions (Matisse convention), with junction IDs as column names. Feed directly to CreateMatisseObject(junction_counts = ...).

Details

STARsolo writes the SJ matrix as junctions x cells with a 9-column features.tsv (chr, intron start, intron end, strand code, splice motif, ...). The intron start/end are the first and last intronic base; the strand code is 0 (undefined), 1 (+) or 2 (-). Only a raw matrix is emitted for SJ, so pass the filtered cell barcodes (e.g. from Gene/filtered) via cells to subset.

See also

BuildJunctionEvents to turn SUPPA2 events into a junction-ID event table that matches these column names.

Examples

if (FALSE) { # \dontrun{
jxn <- ReadSTARsoloSJ("Solo.out/SJ/raw", cells = colnames(seu))
obj <- CreateMatisseObject(seu, junction_counts = jxn,
                           events = BuildJunctionEvents(ioe_files))
} # }