STAR Module Documentation

The STAR (Spliced Transcripts Alignment to a Reference) alignment tool is widely used in genomics research for aligning RNA-seq data to a reference genome. Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635

ensembl.tools.anno.transcriptomic_annotation.star.run_star(genome_file: Path, output_dir: Path, short_read_fastq_dir: Path, delete_pre_trim_fastq: bool = False, trim_fastq: bool = False, max_reads_per_sample: int = 0, max_intron_length: int = 100000, num_threads: int = 1, star_bin: Path = PosixPath('star'), samtools_bin: Path = PosixPath('samtools'), trim_galore_bin: Path = PosixPath('trim_galore')) → None

Run STAR alignment on list of short read data.

param genome_file:

Genome file path.

type genome_file:

Path

param output_dir:

Working directory path.

type output_dir:

Path

param short_read_fastq_dir:

Short read directory path.

type short_read_fastq_dir:

Path

param delete_pre_trim_fastq:

Delete the original fastq files after trimming. Defaults to False.

type delete_pre_trim_fastq:

boolean, default False

param trim_fastq:

Trim short read files using TrimGalore. Defaults to False.

type trim_fastq:

boolean, default False

param max_reads_per_sample:

Max number of reads per sample. Defaults to 0 (unlimited).

type max_reads_per_sample:

int, default 0

param max_intron_length:

The maximum intron size for alignments. Defaults to 100000.

type max_intron_length:

int, default 100000

param num_threads:

Number of available threads.

type num_threads:

int, default 1

param star_bin:

Software path.

type star_bin:

Path, default star

param samtools_bin:

Software path.

type samtools_bin:

Path,default samtools

param trim_galore_bin:

Software path.

type trim_galore_bin:

Path, default trim_galore

return:

None

rtype:

None