maximum and type of allowed allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate

type of read ends alignment

how to flush ambiguous insertion positions

Windows, Anchors, Binning Options

types of quantification requested

desired SAM attributes, in the order desired for the output SAM

different filters for chimeric alignments

type of chimeric output

formatting type for the Chimeric.out.junction file

Genome Indexing Parameters - only used with --runMode genomeGenerate

mode of shared memory usage for the genome files. Only used with --runMode alignReads.

clipping options from either end of the mates

lengths of names,sequences,qualities for both mates are the same / not the same. NotEqual is safe in all situations.

filter alignment using their motifs

filter the output into main SAM/BAM files

mode of SAM output

type of sorting for the SAM output

type of SAM/BAM output

which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG

format of input read files

read ID record type

mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only

type of the STAR run

length of the barcode read

matching the Cell Barcodes to the WhiteList

cell filtering type and parameters

genomic features for which the UMI counts per Cell Barcode are collected

strandedness of the solo libraries:

type of single-cell RNA-seq

type of UMI deduplication (collapsing) algorithm

type of UMI filtering

which files to save when sjdb junctions are inserted on the fly at the mapping step

which reads to consider for collapsed splice junctions output

Cufflinks-like strand field flag

prohibit various alignment type

2-pass mapping mode.

output of unmapped reads in the SAM format

WASP allele-specific output type. This is re-implemenation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061�1063 (2015), https://www.nature.com/articles/nmeth.3582 .

type of signal output, e.g. "bedGraph" OR "bedGraph read1_5p". Requires sorted BAM: --outSAMtype BAM SortedByCoordinate .