dynast.align

Module Contents

Functions

STAR_solo(fastqs, index_dir, out_dir, technology, whitelist_path=None, strand='forward', n_threads=8, temp_dir=None, nasc=False, overrides=None)

Align FASTQs with STARsolo.

align(fastqs, index_dir, out_dir, technology, whitelist_path=None, strand='forward', n_threads=8, temp_dir=None, nasc=False, overrides=None)

dynast.align.STAR_solo(fastqs, index_dir, out_dir, technology, whitelist_path=None, strand='forward', n_threads=8, temp_dir=None, nasc=False, overrides=None)

Align FASTQs with STARsolo.

Parameters

  • fastqs (list) – list of path to FASTQs. Order matters – STAR assumes the UMI and barcode are in read 2

  • index_dir (str) – path to directory containing STAR index

  • out_dir (str) – path to directory to place STAR output

  • technology (collections.namedtuple) – a Technology object defined in technology.py

  • whitelist_path (str, optional) – path to textfile containing barcode whitelist, defaults to None

  • strand (str, optional) – strandedness of the sequencing protocol, defaults to forward, may be one of the following: forward, reverse, unstranded

  • n_threads (int, optional) – number of threads to use, defaults to 8

  • temp_dir (str, optional) – STAR temporary directory, defaults to None, which uses the system temporary directory

  • nasc (bool, optional) – whether or not to use STAR configuration used in NASC-seq pipeline, defaults to False

  • overrides (dictionary, optional) – STAR command-line argument overrides, defaults to None

Returns

dictionary containing output files

Return type

dict

dynast.align.align(fastqs, index_dir, out_dir, technology, whitelist_path=None, strand='forward', n_threads=8, temp_dir=None, nasc=False, overrides=None)