omicverse.alignment.STAR

omicverse.alignment.STAR(samples, genome_dir, output_dir='star', threads=8, memory='50G', jobs=None, max_workers=None, gtf=None, gtf_feature='exon', sjdb_overhang=None, genome_fasta_files=None, auto_index=True, strict=False, genome_generate_threads=None, genome_generate_sjdb_overhang=None, genome_generate_gtf_feature=None, genome_generate_extra_args=None, extra_args=None, star_path=None, auto_install=True, overwrite=False)[source]

Run STAR alignment.

Parameters:

  • samples (Union[Tuple[str, str], Tuple[str, str, Optional[str]], Sequence[Tuple[str, str]], Sequence[Tuple[str, str, Optional[str]]]]) – Single sample tuple (sample, fq1[, fq2]) or list of such tuples.

  • genome_dir (str) – STAR genome index directory.

  • output_dir (str (default: 'star')) – Output directory for per-sample STAR outputs.

  • threads (int (default: 8)) – Threads per STAR job.

  • memory (str (default: '50G')) – Memory limit for BAM sorting (e.g. ‘50G’).

  • jobs (Optional[int] (default: None)) – Concurrent jobs.

  • max_workers (Optional[int] (default: None)) – Legacy alias for jobs.

  • gtf (Optional[str] (default: None)) – Optional GTF for splice junctions.

  • gtf_feature (Optional[str] (default: 'exon')) – GTF feature name for exons (default: exon).

  • sjdb_overhang (Optional[int] (default: None)) – Optional SJDB overhang.

  • genome_fasta_files (Union[str, Sequence[str], None] (default: None)) – FASTA file(s) for auto-building STAR index if missing.

  • auto_index (bool (default: True)) – If True, attempt to build STAR index automatically when missing.

  • strict (bool (default: False)) – If True, raise errors; otherwise return error messages per sample.

  • genome_generate_threads (Optional[int] (default: None)) – Threads for genomeGenerate (defaults to threads).

  • genome_generate_sjdb_overhang (Optional[int] (default: None)) – sjdbOverhang used during genomeGenerate (defaults to sjdb_overhang).

  • genome_generate_gtf_feature (Optional[str] (default: None)) – GTF feature name used during genomeGenerate (defaults to gtf_feature).

  • genome_generate_extra_args (Optional[Sequence[str]] (default: None)) – Extra args for genomeGenerate.

  • extra_args (Optional[Sequence[str]] (default: None)) – Additional STAR CLI arguments.

  • star_path (Optional[str] (default: None)) – Explicit path to STAR executable.

  • auto_install (bool (default: True)) – Install missing tools automatically when possible.

  • overwrite (bool (default: False)) – If True, rerun STAR and overwrite existing outputs.

Return type:

Union[Dict[str, str], List[Dict[str, str]]]