Question: What parameters are used for STAR alignment?
Answer: Cell Ranger uses STAR for alignment, and most parameters for alignment are set to the default values. Below are the STAR parameters used in Cell Ranger:
args = [
'STAR', '--genomeDir', self.reference_star_path,
'--outSAMmultNmax', str(max_report_alignments_per_read),
'--runThreadN', str(threads),
'--readNameSeparator', 'space',
'--outSAMunmapped', 'Within', 'KeepPairs',
'--outSAMtype', 'SAM',
'--outStd', 'SAM',
'--outSAMorder', 'PairedKeepInputOrder',
]
Relevant code can be found in the source code here. This code is for an older Cell Ranger version (v3). However, no changes have been made to the above parameters in later versions of Cell Ranger. For parameters not listed, default values are used.
For the STAR parameter --outSAMmultNmax, you can search within the code for max_report_alignments_per_read to find:
max_report_alignments_per_read=-1