Table 1.

Parameter	Description and allowed values
Filtering of output alignments
--outFilterType	type of filtering. Normal [default]: standard filtering using only current alignment BySJout: keep only those reads that contain junctions that passed filtering into SJ.out.tab
--outFilterMultimapScoreRange	the score range below the maximum score for multimapping alignments [default=1]
--outFilterMultimapNmax	read alignments will be output only if the read maps is less or equal than this value, otherwise no alignments will be output [default=10]
--outFilterMismatchNmax	alignment will be output only if it has <= mismatches than this value [default=10]
--outFilterMismatchNoverLmax	same as --outFilterMismatchNmax, but normalized to the mapped length is than this value [default=0.3]
--outFilterMismatchNoverReadLmax	same as --outFilterMismatchNmax, but normalized to the full read length [default=1]
--outFilterScoreMin	alignment will be output only if its alignment score is greater or equal than this value [default=0]
--outFilterScoreMinOverLread	same as --outFilterScoreMin, but normalized to read length [default=0.66]
--outFilterMatchNmin	alignment will be output only if the number of matched bases is greater or equal than this value [default=0]
--outFilterMatchNminOverLread	same as --outFilterMatchNminOverLread, but normalized to the read length [default=.066]
Search sensitivity
--seedSearchStartLmax	defines the search start point through the read - the read is split into pieces no longer than this value [default=50]
Spliced alignments
--alignIntronMin	minimum intron size: genomic gap is considered intron if its length greater or equal than this value, otherwise it is considered deletion [default=21]
--alignIntronMax	maximum intron size. [default=0] => max intron size will be determined by (2ˆwinBinNbits)*winAnchorDistNbins
--alignMatesGapMax	maximum gap between two mates, [default=0] => max intron gap will be determined by (2ˆwinBinNbits)*winAnchorDistNbins
--alignSJoverhangMin	minimum overhang for spliced alignments [default=5]
--alignSJDBoverhangMin	minimum mapped length for a read mate that is spliced [default=5]