dynast.align
Module Contents
Functions
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Align FASTQs with STARsolo. |
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Main interface for the align command. |
- dynast.align.STAR_solo(fastqs: List[str], index_dir: str, out_dir: str, technology: dynast.technology.Technology, whitelist_path: Optional[str] = None, strand: typing_extensions.Literal[forward, reverse, unstranded] = 'forward', n_threads: int = 8, temp_dir: Optional[str] = None, nasc: bool = False, overrides: Optional[Dict[str, str]] = None) Dict[str, str][source]
Align FASTQs with STARsolo.
- Parameters
- fastqs
List of path to FASTQs. Order matters – STAR assumes the UMI and barcode are in read 2
- index_dir
Path to directory containing STAR index
- out_dir
Path to directory to place STAR output
- technology
Technology specification
- whitelist_path
Path to textfile containing barcode whitelist
- strand
Strandedness of the sequencing protocol may be one of the following: forward, reverse, unstranded
- n_threads
Number of threads to use
- temp_dir
STAR temporary directory, defaults to None, which uses the system temporary directory
- nasc
Whether or not to use STAR configuration used in NASC-seq pipeline
- overrides
STAR command-line argument overrides
- dynast.align.align(fastqs: List[str], index_dir: str, out_dir: str, technology: dynast.technology.Technology, whitelist_path: Optional[str] = None, strand: typing_extensions.Literal[forward, reverse, unstranded] = 'forward', n_threads: int = 8, temp_dir: Optional[str] = None, nasc: bool = False, overrides: Optional[Dict[str, str]] = None)[source]
Main interface for the align command.
- Parameters
- fastqs
List of path to FASTQs. Order matters – STAR assumes the UMI and barcode are in read 2
- index_dir
Path to directory containing STAR index
- out_dir
Path to directory to place STAR output
- technology
Technology specification
- whitelist_path
Path to textfile containing barcode whitelist
- strand
Strandedness of the sequencing protocol may be one of the following: forward, reverse, unstranded
- n_threads
Number of threads to use
- temp_dir
STAR temporary directory, defaults to None, which uses the system temporary directory
- nasc
Whether or not to use STAR configuration used in NASC-seq pipeline
- overrides
STAR command-line argument overrides