genomeLoad NoSharedMemory
outSAMtype BAM Unsorted
outSAMstrandField intronMotif
outSAMattributes NH HI AS NM MD MC
outSAMunmapped Within KeepPairs
outFilterMultimapNmax 50
peOverlapNbasesMin 10
alignSplicedMateMapLminOverLmate 0.5
alignSJstitchMismatchNmax 5 -1 5 5
chimSegmentMin 10
chimOutType WithinBAM HardClip
chimJunctionOverhangMin 10
chimScoreDropMax 30
chimScoreJunctionNonGTAG 0
chimScoreSeparation 1
chimSegmentReadGapMax 3
chimMultimapNmax 50
