What parameters are used for STAR index?

Question: What parameters are used for STAR index?

Answer: You can find more information about the STAR parameters used by Cell Ranger in the source code. The relevant files are:

cellranger-x.y.z/cellranger-cs/x.y.z/lib/python/cellranger/reference.py
cellranger-x.y.z/cellranger-cs/x.y.z/mro/stages/counter/align_reads/__init__.py

where x.y.z indicates the Cell Ranger version.

For example, the following piece of code in lib/python/cellranger/reference.py has STAR index parameters:

args = ['STAR', '--runMode', 'genomeGenerate', '--genomeDir', self.reference_star_path,
'--runThreadN', str(num_threads), '--genomeFastaFiles', in_fasta_fn,
'--sjdbGTFfile', in_gtf_fn]
if limit_ram is not None:
    args += ['--limitGenomeGenerateRAM', str(limit_ram)]
if sa_sparse_d is not None:
    args += ['--genomeSAsparseD', str(sa_sparse_d)]
if sa_index_n_bases is not None:
    args += ['--genomeSAindexNbases', str(sa_index_n_bases)]
if chr_bin_n_bits is not None:
    args += ['--genomeChrBinNbits', str(chr_bin_n_bits)]

Note: The --limitGenomeGenerateRAMwithin STAR, limits the maximum memory for genome generation. Within cellranger mkref pipeline this can be throttled using the --memgbparameter (default, --memgb=16GB). 

For the STAR parameter --genomeChrBinNbits, you can search within this file for 'chr_bin_n_bits' to find:

chr_bin_n_bits = min(18, int(math.log(genome_size_b/genome_num_chrs, 2)))

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