Star#
The STAR (Spliced Transcripts Alignment to a Reference) alignment tool is widely used
API#
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.
References
[8]
- ensembl.tools.anno.transcriptomic_annotation.star.run_star(genome_file, output_dir, short_read_fastq_dir, delete_pre_trim_fastq=False, trim_fastq=False, max_reads_per_sample=0, max_intron_length=100000, subsample_read_limit=100000000, subsample_percentage=0.25, sampling_via_read_limit=False, sampling_via_percentage=False, sampling_via_read_limit_percentage=False, num_threads=1, star_bin=PosixPath('STAR'), samtools_bin=PosixPath('samtools'), trim_galore_bin=PosixPath('trim_galore'))[source]#
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 subsample_read_limit:
Maximum number of reads to subsample. Defaults to 100000000.
:type subsample_read_limit:int, default 100000000, :param subsample_percentage: Maximun percentage of reads to subsample. :type subsample_percentage: int, default 0.25, :param sampling_via_read_limit: subsample fastq files using subsample_read_limit. :type sampling_via_read_limit: boolean, False, :param sampling_via_percentage: subsample fastq files using subsample_percentage. :type sampling_via_percentage: boolean, False, :param sampling_via_read_limit_percentage: use max read limit and percentage value. :type sampling_via_read_limit_percentage: boolean, False, :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
- Parameters:
genome_file (Path)
output_dir (Path)
short_read_fastq_dir (Path)
delete_pre_trim_fastq (bool)
trim_fastq (bool)
max_reads_per_sample (int)
max_intron_length (int)
subsample_read_limit (int)
subsample_percentage (float)
sampling_via_read_limit (bool)
sampling_via_percentage (bool)
sampling_via_read_limit_percentage (bool)
num_threads (int)
star_bin (Path)
samtools_bin (Path)
trim_galore_bin (Path)
- Return type:
None
- ensembl.tools.anno.transcriptomic_annotation.star.subsample_transcriptomic_data(fastq_file_list, subsample_read_limit=100000000, subsample_percentage=0.25, sampling_via_read_limit=False, sampling_via_percentage=False, sampling_via_read_limit_percentage=True, num_threads=2)[source]#
Subsample list of paired files. Args:
fastq_file_list : Subsample paired fastq files. subsample_read_limit : Maximum number of reads to subsample, default to 100000000. subsample_percentage : Maximun percentage of reads to subsample, default to 0.25. sampling_via_read_limit : If True will subsample an input dataset of fastq files using –subsample_read_limit value. sampling_via_percentage : If True will subsample an input dataset of fastq files using –subsample_percentage value. sampling_via_read_limit_percentage : If True will subsample an input dataset of fastq files using –subsample_read_limit and –subsample_percentage value; the lowest number of reads is taken. num_threads : number of threads
- Returns:
List[Path]: List of subsampled paired transcriptomic files
- ensembl.tools.anno.transcriptomic_annotation.star.run_trimming(output_dir, short_read_fastq_dir, delete_pre_trim_fastq=False, num_threads=1, trim_galore_bin=PosixPath('trim_galore'))[source]#
Trim list of short read fastq files. Args:
output_dir : Working directory path. short_read_fastq_dir : Short read directory path. delete_pre_trim_fastq : Removing original fastq file post trimming. Defaults to False. num_threads : Number of threads. trim_galore_bin : Software path.