STAR_Parameters_Endogenous_smallRNA.in

runMode  alignReads
outSAMtype  BAM Unsorted
#outSAMtype  BAM SortedByCoordinate
outSAMattributes  All
#outFilterMismatchNmax  1
#outFilterMismatchNoverLmax  0.1
#outFilterMismatchNoverLmax  0.03
outFilterMismatchNoverLmax  0.05
outFilterMatchNmin  16
readFilesCommand  zcat
outSAMunmapped  None
outReadsUnmapped  Fastx
outFilterMultimapNmax  1000000
#alignEndsType  EndToEnd
alignEndsType  Local
# disable splicing
alignIntronMax  1
alignIntronMin  2