\optSection{Parameter Files}\label{Parameter_Files}
\begin{optTable}
\optName{parametersFiles}
  \optValue{-}
  \optLine{string: name of a user-defined parameters file, "-": none. Can only be defined on the command line.} 
\end{optTable}
\optSection{System}\label{System}
\begin{optTable}
\optName{sysShell}
  \optValue{-}
  \optLine{string: path to the shell binary, preferrably bash, e.g. /bin/bash. } 
\begin{optOptTable}
  \optOpt{-}   \optOptLine{the default shell is executed, typically /bin/sh. This was reported to fail on some Ubuntu systems - then you need to specify path to bash.}
\end{optOptTable}
\end{optTable}
\optSection{Run Parameters}\label{Run_Parameters}
\begin{optTable}
\optName{runMode}
  \optValue{alignReads}
  \optLine{string: type of the run:    } 
\begin{optOptTable}
  \optOpt{alignReads}   \optOptLine{map reads}
  \optOpt{genomeGenerate}   \optOptLine{generate genome files}
  \optOpt{inputAlignmentsFromBAM}   \optOptLine{input alignments from BAM. Presently only works with --outWigType and --bamRemoveDuplicates.}
\end{optOptTable}
\optName{runThreadN}
  \optValue{1}
  \optLine{int: number of threads to run STAR} 
\optName{runDirPerm}
  \optValue{User{\textunderscore}RWX}
  \optLine{string: permissions for the directories created at the run-time. } 
\begin{optOptTable}
  \optOpt{User{\textunderscore}RWX}   \optOptLine{user-read/write/execute}
  \optOpt{All{\textunderscore}RWX}   \optOptLine{all-read/write/execute (same as chmod 777)}
\end{optOptTable}
\optName{runRNGseed}
  \optValue{777}
  \optLine{int: random number generator seed.} 
\end{optTable}
\optSection{Genome Parameters}\label{Genome_Parameters}
\begin{optTable}
\optName{genomeDir}
  \optValue{./GenomeDir/}
  \optLine{string: path to the directory where genome files are stored (if runMode!=generateGenome) or will be generated (if runMode==generateGenome)} 
\optName{genomeLoad}
  \optValue{NoSharedMemory}
  \optLine{string: mode of shared memory usage for the genome files} 
\begin{optOptTable}
  \optOpt{LoadAndKeep}   \optOptLine{load genome into shared and keep it in memory after run}
  \optOpt{LoadAndRemove}   \optOptLine{load genome into shared but remove it after run}
  \optOpt{LoadAndExit}   \optOptLine{load genome into shared memory and exit, keeping the genome in memory for future runs}
  \optOpt{Remove}   \optOptLine{do not map anything, just remove loaded genome from memory}
  \optOpt{NoSharedMemory}   \optOptLine{do not use shared memory, each job will have its own private copy of the genome}
\end{optOptTable}
\end{optTable}
\optSection{Genome Generation Parameters}\label{Genome_Generation_Parameters}
\begin{optTable}
\optName{genomeFastaFiles}
  \optValue{-}
  \optLine{string(s): path(s) to the fasta files with genomic sequences for genome generation, separated by spaces. Only used if runMode==genomeGenerate. These files should be plain text FASTA files, they *cannot* be zipped.} 
\optName{genomeChrBinNbits}
  \optValue{18}
  \optLine{int: =log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins} 
\optName{genomeSAindexNbases}
  \optValue{14}
  \optLine{int: length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches.} 
\optName{genomeSAsparseD}
  \optValue{1}
  \optLine{int{\textgreater}0: suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction} 
\optName{genomeSuffixLengthMax}
  \optValue{-1}
  \optLine{int: maximum length of the suffixes, has to be longer than read length. -1 = infinite.} 
\end{optTable}
\optSection{Splice Junctions Database}\label{Splice_Junctions_Database}
\begin{optTable}
\optName{sjdbFileChrStartEnd}
  \optValue{-}
  \optLine{string(s): path to the files with genomic coordinates (chr {\textless}tab{\textgreater} start {\textless}tab{\textgreater} end {\textless}tab{\textgreater} strand) for the splice junction introns. Multiple files can be supplied wand will be concatenated.} 
\optName{sjdbGTFfile}
  \optValue{-}
  \optLine{string: path to the GTF file with annotations} 
\optName{sjdbGTFchrPrefix}
  \optValue{-}
  \optLine{string: prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC geneomes)} 
\optName{sjdbGTFfeatureExon}
  \optValue{exon}
  \optLine{string: feature type in GTF file to be used as exons for building transcripts} 
\optName{sjdbGTFtagExonParentTranscript}
  \optValue{transcript{\textunderscore}id}
  \optLine{string: tag name to be used as exons' transcript-parents (default "transcript{\textunderscore}id" works for GTF files)} 
\optName{sjdbGTFtagExonParentGene}
  \optValue{gene{\textunderscore}id}
  \optLine{string: tag name to be used as exons' gene-parents (default "gene{\textunderscore}id" works for GTF files)} 
\optName{sjdbOverhang}
  \optValue{100}
  \optLine{int{\textgreater}0: length of the donor/acceptor sequence on each side of the junctions, ideally = (mate{\textunderscore}length - 1)} 
\optName{sjdbScore}
  \optValue{2}
  \optLine{int: extra alignment score for alignmets that cross database junctions} 
\optName{sjdbInsertSave}
  \optValue{Basic}
  \optLine{string: which files to save when sjdb junctions are inserted on the fly at the mapping step} 
\begin{optOptTable}
  \optOpt{Basic}   \optOptLine{only small junction / transcript files}
  \optOpt{All}   \optOptLine{all files including big Genome, SA and SAindex - this will create a complete genome directory}
\end{optOptTable}
\end{optTable}
\optSection{Input Files}\label{Input_Files}
\begin{optTable}
\optName{inputBAMfile}
  \optValue{-}
  \optLine{string: path to BAM input file, to be used with --runMode inputAlignmentsFromBAM} 
\end{optTable}
\optSection{Read Parameters}\label{Read_Parameters}
\begin{optTable}
\optName{readFilesIn}
  \optValue{Read1 Read2}
  \optLine{string(s): paths to files that contain input read1 (and, if needed,  read2)} 
\optName{readFilesCommand}
  \optValue{-}
  \optLine{string(s): command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout} 
  \optLine{For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc.} 
\optName{readMapNumber}
  \optValue{-1}
  \optLine{int: number of reads to map from the beginning of the file} 
  \optLine{-1: map all reads} 
\optName{readMatesLengthsIn}
  \optValue{NotEqual}
  \optLine{string: Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same  / not the same. NotEqual is safe in all situations.} 
\optName{readNameSeparator}
  \optValue{/}
  \optLine{string(s): character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed)} 
\optName{clip3pNbases}
  \optValue{0}
  \optLine{int(s): number(s) of bases to clip from 3p of each mate. If one value is given, it will be assumed the same for both mates.} 
\optName{clip5pNbases}
  \optValue{0}
  \optLine{int(s): number(s) of bases to clip from 5p of each mate. If one value is given, it will be assumed the same for both mates.} 
\optName{clip3pAdapterSeq}
  \optValue{-}
  \optLine{string(s): adapter sequences to clip from 3p of each mate.  If one value is given, it will be assumed the same for both mates.} 
\optName{clip3pAdapterMMp}
  \optValue{0.1}
  \optLine{double(s): max proportion of mismatches for 3p adpater clipping for each mate.  If one value is given, it will be assumed the same for both mates.} 
\optName{clip3pAfterAdapterNbases}
  \optValue{0}
  \optLine{int(s): number of bases to clip from 3p of each mate after the adapter clipping. If one value is given, it will be assumed the same for both mates.} 
\end{optTable}
\optSection{Limits}\label{Limits}
\begin{optTable}
\optName{limitGenomeGenerateRAM}
  \optValue{31000000000}
  \optLine{int{\textgreater}0: maximum available RAM (bytes) for genome generation} 
\optName{limitIObufferSize}
  \optValue{150000000}
  \optLine{int{\textgreater}0: max available buffers size (bytes) for input/output, per thread} 
\optName{limitOutSAMoneReadBytes}
  \optValue{100000}
  \optLine{int{\textgreater}0: max size of the SAM record for one read. Recommended value: {\textgreater}(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax} 
\optName{limitOutSJoneRead}
  \optValue{1000}
  \optLine{int{\textgreater}0: max number of junctions for one read (including all multi-mappers)} 
\optName{limitOutSJcollapsed}
  \optValue{1000000}
  \optLine{int{\textgreater}0: max number of collapsed junctions} 
\optName{limitBAMsortRAM}
  \optValue{0}
  \optLine{int{\textgreater}=0: maximum available RAM for sorting BAM. If =0, it will be set to the genome index size. 0 value can only be used with --genomeLoad NoSharedMemory option.} 
\optName{limitSjdbInsertNsj}
  \optValue{1000000}
  \optLine{int{\textgreater}=0: maximum number of junction to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run} 
\end{optTable}
\optSection{Output: general}\label{Output:_general}
\begin{optTable}
\optName{outFileNamePrefix}
  \optValue{./}
  \optLine{string: output files name prefix (including full or relative path). Can only be defined on the command line.} 
\optName{outTmpDir}
  \optValue{-}
  \optLine{string: path to a directory that will be used as temporary by STAR. All contents of this directory will be removed!} 
  \optLine{- the temp directory will default to outFileNamePrefix{\textunderscore}STARtmp} 
\optName{outStd}
  \optValue{Log}
  \optLine{string: which output will be directed to stdout (standard out)} 
\begin{optOptTable}
  \optOpt{Log}   \optOptLine{log messages}
  \optOpt{SAM}   \optOptLine{alignments in SAM format (which normally are output to Aligned.out.sam file), normal standard output will go into Log.std.out}
  \optOpt{BAM{\textunderscore}Unsorted}   \optOptLine{alignments in BAM format, unsorted. Requires --outSAMtype BAM Unsorted}
  \optOpt{BAM{\textunderscore}SortedByCoordinate}   \optOptLine{alignments in BAM format, unsorted. Requires --outSAMtype BAM SortedByCoordinate}
  \optOpt{BAM{\textunderscore}Quant}   \optOptLine{alignments to transcriptome in BAM format, unsorted. Requires --quantMode TranscriptomeSAM}
\end{optOptTable}
\optName{outReadsUnmapped}
  \optValue{None}
  \optLine{string: output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s).} 
\begin{optOptTable}
  \optOpt{None}   \optOptLine{no output}
  \optOpt{Fastx}   \optOptLine{output in separate fasta/fastq files, Unmapped.out.mate1/2}
\end{optOptTable}
\optName{outQSconversionAdd}
  \optValue{0}
  \optLine{int: add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31)} 
\optName{outMultimapperOrder}
  \optValue{Old{\textunderscore}2.4}
  \optLine{string: order of multimapping alignments in the output files} 
\begin{optOptTable}
  \optOpt{Old{\textunderscore}2.4}   \optOptLine{quasi-random order used before 2.5.0}
  \optOpt{Random}   \optOptLine{random order of alignments for each multi-mapper. Read mates (pairs) are always adjacent, all alignment for each read stay together. This option will become default in the future releases.}
\end{optOptTable}
\end{optTable}
\optSection{Output: SAM and BAM}\label{Output:_SAM_and_BAM}
\begin{optTable}
\optName{outSAMtype}
  \optValue{SAM}
  \optLine{strings: type of SAM/BAM output} 
  \optLine{1st word: } 
\begin{optOptTable}
  \optOpt{BAM}   \optOptLine{output BAM without sorting}
  \optOpt{SAM}   \optOptLine{output SAM without sorting}
  \optOpt{None}   \optOptLine{no SAM/BAM output}
\end{optOptTable}
  \optLine{2nd, 3rd: } 
\begin{optOptTable}
  \optOpt{Unsorted}   \optOptLine{standard unsorted}
  \optOpt{SortedByCoordinate}   \optOptLine{sorted by coordinate. This option will allocate extra memory for sorting which can be specified by --limitBAMsortRAM.}
\end{optOptTable}
\optName{outSAMmode}
  \optValue{Full}
  \optLine{string: mode of SAM output  } 
\begin{optOptTable}
  \optOpt{None}   \optOptLine{no SAM output}
  \optOpt{Full}   \optOptLine{full SAM output}
  \optOpt{NoQS}   \optOptLine{full SAM but without quality scores}
\end{optOptTable}
\optName{outSAMstrandField}
  \optValue{None}
  \optLine{string: Cufflinks-like strand field flag} 
\begin{optOptTable}
  \optOpt{None}   \optOptLine{not used}
  \optOpt{intronMotif}   \optOptLine{strand derived from the intron motif. Reads with inconsistent and/or non-canonical introns are filtered out.}
\end{optOptTable}
\optName{outSAMattributes}
  \optValue{Standard}
  \optLine{string: a string of desired SAM attributes, in the order desired for the output SAM} 
\begin{optOptTable}
  \optOpt{NH}   \optOptLine{any combination in any order}
  \optOpt{Standard}   \optOptLine{NH HI AS nM }
  \optOpt{All}   \optOptLine{NH HI AS nM NM MD jM jI}
  \optOpt{None}   \optOptLine{no attributes}
\end{optOptTable}
\optName{outSAMattrIHstart}
  \optValue{1}
  \optLine{int{\textgreater}=0:                     start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie.} 
\optName{outSAMunmapped}
  \optValue{None}
  \optLine{string(s): output of unmapped reads in the SAM format} 
  \optLine{1st word:} 
\begin{optOptTable}
  \optOpt{None}   \optOptLine{no output}
  \optOpt{Within}   \optOptLine{output unmapped reads within the main SAM file (i.e. Aligned.out.sam)}
\end{optOptTable}
  \optLine{2nd word:} 
\begin{optOptTable}
  \optOpt{KeepPairs}   \optOptLine{record unmapped mate for each alignment, and, in case of unsroted output, keep it adjacent to its mapped mate.}
\end{optOptTable}
  \optLine{Only affects multi-mapping reads} 
\optName{outSAMorder}
  \optValue{Paired}
  \optLine{string: type of sorting for the SAM output} 
  \optLine{Paired: one mate after the other for all paired alignments} 
  \optLine{PairedKeepInputOrder: one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files} 
\optName{outSAMprimaryFlag}
  \optValue{OneBestScore}
  \optLine{string: which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG} 
\begin{optOptTable}
  \optOpt{OneBestScore}   \optOptLine{only one alignment with the best score is primary}
  \optOpt{AllBestScore}   \optOptLine{all alignments with the best score are primary}
\end{optOptTable}
\optName{outSAMreadID}
  \optValue{Standard}
  \optLine{string: read ID record type} 
\begin{optOptTable}
  \optOpt{Standard}   \optOptLine{first word (until space) from the FASTx read ID line, removing /1,/2 from the end}
  \optOpt{Number}   \optOptLine{read number (index) in the FASTx file}
\end{optOptTable}
\optName{outSAMmapqUnique}
  \optValue{255}
  \optLine{int: 0 to 255: the MAPQ value for unique mappers} 
\optName{outSAMflagOR}
  \optValue{0}
  \optLine{int: 0 to 65535: sam FLAG will be bitwise OR'd with this value, i.e. FLAG=FLAG | outSAMflagOR. This is applied after all flags have been set by STAR, and after outSAMflagAND. Can be used to set specific bits that are not set otherwise.} 
\optName{outSAMflagAND}
  \optValue{65535}
  \optLine{int: 0 to 65535: sam FLAG will be bitwise AND'd with this value, i.e. FLAG=FLAG {\&} outSAMflagOR. This is applied after all flags have been set by STAR, but before outSAMflagOR. Can be used to unset specific bits that are not set otherwise.} 
\optName{outSAMattrRGline}
  \optValue{-}
  \optLine{string(s): SAM/BAM read group line. The first word contains the read group identifier and must start with "ID:", e.g. --outSAMattrRGline ID:xxx CN:yy "DS:z z z". } 
  \optLine{xxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted.} 
  \optLine{Comma separated RG lines correspons to different (comma separated) input files in --readFilesIn. Commas have to be surrounded by spaces, e.g.} 
  \optLine{--outSAMattrRGline ID:xxx , ID:zzz "DS:z z" , ID:yyy DS:yyyy} 
\optName{outSAMheaderHD}
  \optValue{-}
  \optLine{strings: @HD (header) line of the SAM header} 
\optName{outSAMheaderPG}
  \optValue{-}
  \optLine{strings: extra @PG (software) line of the SAM header (in addition to STAR)} 
\optName{outSAMheaderCommentFile}
  \optValue{-}
  \optLine{string: path to the file with @CO (comment) lines of the SAM header} 
\optName{outSAMfilter}
  \optValue{None}
  \optLine{string(s): filter the output into main SAM/BAM files} 
\begin{optOptTable}
  \optOpt{KeepOnlyAddedReferences}   \optOptLine{only keep the reads for which all alignments are to the extra reference sequences added with --genomeFastaFiles at the mapping stage.}
\end{optOptTable}
\optName{outSAMmultNmax}
  \optValue{-1}
  \optLine{int: max number of multiple alignments for a read that will be output to the SAM/BAM files.} 
\begin{optOptTable}
  \optOpt{-1}   \optOptLine{all alignments (up to --outFilterMultimapNmax) will be output}
\end{optOptTable}
\optName{outBAMcompression}
  \optValue{1}
  \optLine{int: -1 to 10  BAM compression level, -1=default compression (6?), 0=no compression, 10=maximum compression} 
\optName{outBAMsortingThreadN}
  \optValue{0}
  \optLine{int: {\textgreater}=0: number of threads for BAM sorting. 0 will default to min(6,--runThreadN).} 
\end{optTable}
\optSection{BAM processing}\label{BAM_processing}
\begin{optTable}
\optName{bamRemoveDuplicatesType}
  \optValue{-}
  \optLine{string: mark duplicates in the BAM file, for now only works with sorted BAM feeded with inputBAMfile} 
\begin{optOptTable}
  \optOpt{-}   \optOptLine{no duplicate removal/marking}
  \optOpt{UniqueIdentical}   \optOptLine{mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical}
\end{optOptTable}
\optName{bamRemoveDuplicatesMate2basesN}
  \optValue{0}
  \optLine{int{\textgreater}0: number of bases from the 5' of mate 2 to use in collapsing (e.g. for RAMPAGE)} 
\end{optTable}
\optSection{Output Wiggle}\label{Output_Wiggle}
\begin{optTable}
\optName{outWigType}
  \optValue{None}
  \optLine{string(s): type of signal output, e.g. "bedGraph" OR "bedGraph read1{\textunderscore}5p". Requires sorted BAM: --outSAMtype BAM SortedByCoordinate .} 
  \optLine{1st word:} 
\begin{optOptTable}
  \optOpt{None}   \optOptLine{no signal output}
  \optOpt{bedGraph}   \optOptLine{bedGraph format }
  \optOpt{wiggle}   \optOptLine{wiggle format}
\end{optOptTable}
  \optLine{2nd word:} 
\begin{optOptTable}
  \optOpt{read1{\textunderscore}5p}   \optOptLine{signal from only 5' of the 1st read, useful for CAGE/RAMPAGE etc}
  \optOpt{read2}   \optOptLine{signal from only 2nd read}
\end{optOptTable}
\optName{outWigStrand}
  \optValue{Stranded}
  \optLine{string: strandedness of wiggle/bedGraph output} 
\begin{optOptTable}
  \optOpt{Stranded}   \optOptLine{separate strands, str1 and str2}
  \optOpt{Unstranded}   \optOptLine{collapsed strands}
\end{optOptTable}
\optName{outWigReferencesPrefix}
  \optValue{-}
  \optLine{string: prefix matching reference names to include in the output wiggle file, e.g. "chr", default "-" - include all references} 
\optName{outWigNorm}
  \optValue{RPM}
  \optLine{string: type of normalization for the signal} 
\begin{optOptTable}
  \optOpt{RPM}   \optOptLine{reads per million of mapped reads}
  \optOpt{None}   \optOptLine{no normalization, "raw" counts}
\end{optOptTable}
\end{optTable}
\optSection{Output Filtering}\label{Output_Filtering}
\begin{optTable}
\optName{outFilterType}
  \optValue{Normal}
  \optLine{string: type of filtering} 
\begin{optOptTable}
  \optOpt{Normal}   \optOptLine{standard filtering using only current alignment}
  \optOpt{BySJout}   \optOptLine{keep only those reads that contain junctions that passed filtering into SJ.out.tab}
\end{optOptTable}
\optName{outFilterMultimapScoreRange}
  \optValue{1}
  \optLine{int: the score range below the maximum score for multimapping alignments} 
\optName{outFilterMultimapNmax}
  \optValue{10}
  \optLine{int: maximum number of loci the read is allowed to map to. Alignments (all of them) will be output only if the read maps to no more loci than this value. } 
  \optLine{Otherwise no alignments will be output, and the read will be counted as "mapped to too many loci" in the Log.final.out .} 
\optName{outFilterMismatchNmax}
  \optValue{10}
  \optLine{int: alignment will be output only if it has no more mismatches than this value.} 
\optName{outFilterMismatchNoverLmax}
  \optValue{0.3}
  \optLine{float: alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value.} 
\optName{outFilterMismatchNoverReadLmax}
  \optValue{1.0}
  \optLine{float: alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value.} 
\optName{outFilterScoreMin}
  \optValue{0}
  \optLine{int: alignment will be output only if its score is higher than or equal to this value.} 
\optName{outFilterScoreMinOverLread}
  \optValue{0.66}
  \optLine{float: same as outFilterScoreMin, but  normalized to read length (sum of mates' lengths for paired-end reads)} 
\optName{outFilterMatchNmin}
  \optValue{0}
  \optLine{int: alignment will be output only if the number of matched bases is higher than or equal to this value.} 
\optName{outFilterMatchNminOverLread}
  \optValue{0.66}
  \optLine{float: sam as outFilterMatchNmin, but normalized to the read length (sum of mates' lengths for paired-end reads).} 
\optName{outFilterIntronMotifs}
  \optValue{None}
  \optLine{string: filter alignment using their motifs} 
\begin{optOptTable}
  \optOpt{None}   \optOptLine{no filtering}
  \optOpt{RemoveNoncanonical}   \optOptLine{filter out alignments that contain non-canonical junctions}
  \optOpt{RemoveNoncanonicalUnannotated}   \optOptLine{filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept.}
\end{optOptTable}
\end{optTable}
\optSection{Output Filtering: Splice Junctions}\label{Output_Filtering:_Splice_Junctions}
\begin{optTable}
\optName{outSJfilterReads}
  \optValue{All}
  \optLine{string: which reads to consider for collapsed splice junctions output} 
  \optLine{All: all reads, unique- and multi-mappers} 
  \optLine{Unique: uniquely mapping reads only} 
\optName{outSJfilterOverhangMin}
  \optValue{30 12 12 12}
  \optLine{4 integers:    minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif} 
  \optLine{does not apply to annotated junctions} 
\optName{outSJfilterCountUniqueMin}
  \optValue{3 1 1 1}
  \optLine{4 integers: minimum uniquely mapping read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif} 
  \optLine{Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied} 
  \optLine{does not apply to annotated junctions} 
\optName{outSJfilterCountTotalMin}
  \optValue{3 1 1 1}
  \optLine{4 integers: minimum total (multi-mapping+unique) read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif} 
  \optLine{Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied} 
  \optLine{does not apply to annotated junctions} 
\optName{outSJfilterDistToOtherSJmin}
  \optValue{10 0 5 10}
  \optLine{4 integers{\textgreater}=0: minimum allowed distance to other junctions' donor/acceptor} 
  \optLine{does not apply to annotated junctions} 
\optName{outSJfilterIntronMaxVsReadN}
  \optValue{50000 100000 200000}
  \optLine{N integers{\textgreater}=0: maximum gap allowed for junctions supported by 1,2,3,,,N reads } 
  \optLine{i.e. by default junctions supported by 1 read can have gaps {\textless}=50000b, by 2 reads: {\textless}=100000b, by 3 reads: {\textless}=200000. by {\textgreater}=4 reads any gap {\textless}=alignIntronMax} 
  \optLine{does not apply to annotated junctions} 
\end{optTable}
\optSection{Scoring}\label{Scoring}
\begin{optTable}
\optName{scoreGap}
  \optValue{0}
  \optLine{int: splice junction penalty (independent on intron motif)} 
\optName{scoreGapNoncan}
  \optValue{-8}
  \optLine{int: non-canonical junction penalty (in addition to scoreGap)} 
\optName{scoreGapGCAG}
  \optValue{-4}
  \optLine{GC/AG and CT/GC junction penalty (in addition to scoreGap)} 
\optName{scoreGapATAC}
  \optValue{-8}
  \optLine{AT/AC  and GT/AT junction penalty  (in addition to scoreGap)} 
\optName{scoreGenomicLengthLog2scale}
  \optValue{-0.25}
  \optLine{extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)} 
\optName{scoreDelOpen}
  \optValue{-2}
  \optLine{deletion open penalty} 
\optName{scoreDelBase}
  \optValue{-2}
  \optLine{deletion extension penalty per base (in addition to scoreDelOpen)} 
\optName{scoreInsOpen}
  \optValue{-2}
  \optLine{insertion open penalty} 
\optName{scoreInsBase}
  \optValue{-2}
  \optLine{insertion extension penalty per base (in addition to scoreInsOpen)} 
\optName{scoreStitchSJshift}
  \optValue{1}
  \optLine{maximum score reduction while searching for SJ boundaries inthe stitching step} 
\end{optTable}
\optSection{Alignments and Seeding}\label{Alignments_and_Seeding}
\begin{optTable}
\optName{seedSearchStartLmax}
  \optValue{50}
  \optLine{int{\textgreater}0: defines the search start point through the read - the read is split into pieces no longer than this value} 
\optName{seedSearchStartLmaxOverLread}
  \optValue{1.0}
  \optLine{float: seedSearchStartLmax normalized to read length (sum of mates' lengths for paired-end reads)} 
\optName{seedSearchLmax}
  \optValue{0}
  \optLine{int{\textgreater}=0: defines the maximum length of the seeds, if =0 max seed lengthis infinite} 
\optName{seedMultimapNmax}
  \optValue{10000}
  \optLine{int{\textgreater}0: only pieces that map fewer than this value are utilized in the stitching procedure} 
\optName{seedPerReadNmax}
  \optValue{1000}
  \optLine{int{\textgreater}0: max number of seeds per read} 
\optName{seedPerWindowNmax}
  \optValue{50}
  \optLine{int{\textgreater}0: max number of seeds per window} 
\optName{seedNoneLociPerWindow}
  \optValue{10}
  \optLine{int{\textgreater}0: max number of one seed loci per window} 
\optName{alignIntronMin}
  \optValue{21}
  \optLine{minimum intron size: genomic gap is considered intron if its length{\textgreater}=alignIntronMin, otherwise it is considered Deletion} 
\optName{alignIntronMax}
  \optValue{0}
  \optLine{maximum intron size, if 0, max intron size will be determined by (2\^{}winBinNbits)*winAnchorDistNbins} 
\optName{alignMatesGapMax}
  \optValue{0}
  \optLine{maximum gap between two mates, if 0, max intron gap will be determined by (2\^{}winBinNbits)*winAnchorDistNbins} 
\optName{alignSJoverhangMin}
  \optValue{5}
  \optLine{int{\textgreater}0: minimum overhang (i.e. block size) for spliced alignments} 
\optName{alignSJstitchMismatchNmax}
  \optValue{0 -1 0 0}
  \optLine{4*int{\textgreater}=0: maximum number of mismatches for stitching of the splice junctions (-1: no limit). } 
  \optLine{(1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif.} 
\optName{alignSJDBoverhangMin}
  \optValue{3}
  \optLine{int{\textgreater}0: minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments} 
\optName{alignSplicedMateMapLmin}
  \optValue{0}
  \optLine{int{\textgreater}0: minimum mapped length for a read mate that is spliced} 
\optName{alignSplicedMateMapLminOverLmate}
  \optValue{0.66}
  \optLine{float{\textgreater}0: alignSplicedMateMapLmin normalized to mate length} 
\optName{alignWindowsPerReadNmax}
  \optValue{10000}
  \optLine{int{\textgreater}0: max number of windows per read} 
\optName{alignTranscriptsPerWindowNmax}
  \optValue{100}
  \optLine{int{\textgreater}0: max number of transcripts per window           } 
\optName{alignTranscriptsPerReadNmax}
  \optValue{10000}
  \optLine{int{\textgreater}0: max number of different alignments per read to consider} 
\optName{alignEndsType}
  \optValue{Local}
  \optLine{string: type of read ends alignment} 
\begin{optOptTable}
  \optOpt{Local}   \optOptLine{standard local alignment with soft-clipping allowed}
  \optOpt{EndToEnd}   \optOptLine{force end-to-end read alignment, do not soft-clip}
  \optOpt{Extend5pOfRead1}   \optOptLine{fully extend only the 5p of the read1, all other ends: local alignment}
\end{optOptTable}
\optName{alignSoftClipAtReferenceEnds}
  \optValue{Yes}
  \optLine{string: allow the soft-clipping of the alignments past the end of the chromosomes} 
\begin{optOptTable}
  \optOpt{Yes}   \optOptLine{allow}
  \optOpt{No}   \optOptLine{prohibit, useful for compatibility with Cufflinks}
\end{optOptTable}
\end{optTable}
\optSection{Windows, Anchors, Binning}\label{Windows,_Anchors,_Binning}
\begin{optTable}
\optName{winAnchorMultimapNmax}
  \optValue{50}
  \optLine{int{\textgreater}0: max number of loci anchors are allowed to map to} 
\optName{winBinNbits}
  \optValue{16}
  \optLine{int{\textgreater}0: =log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins. } 
\optName{winAnchorDistNbins}
  \optValue{9}
  \optLine{int{\textgreater}0: max number of bins between two anchors that allows aggregation of anchors into one window} 
\optName{winFlankNbins}
  \optValue{4}
  \optLine{int{\textgreater}0: log2(winFlank), where win Flank is the size of the left and right flanking regions for each window} 
\end{optTable}
\optSection{Chimeric Alignments}\label{Chimeric_Alignments}
\begin{optTable}
\optName{chimOutType}
  \optValue{SeparateSAMold}
  \optLine{string: type of chimeric output} 
\begin{optOptTable}
  \optOpt{SeparateSAMold}   \optOptLine{output old SAM into separate Chimeric.out.sam file}
  \optOpt{WithinBAM}   \optOptLine{output into main aligned BAM files (Aligned.*.bam)}
\end{optOptTable}
\optName{chimSegmentMin}
  \optValue{0}
  \optLine{int{\textgreater}=0: minimum length of chimeric segment length, if ==0, no chimeric output} 
\optName{chimScoreMin}
  \optValue{0}
  \optLine{int{\textgreater}=0: minimum total (summed) score of the chimeric segments} 
\optName{chimScoreDropMax}
  \optValue{20}
  \optLine{int{\textgreater}=0: max drop (difference) of chimeric score (the sum of scores of all chimeric segements) from the read length} 
\optName{chimScoreSeparation}
  \optValue{10}
  \optLine{int{\textgreater}=0: minimum difference (separation) between the best chimeric score and the next one} 
\optName{chimScoreJunctionNonGTAG}
  \optValue{-1}
  \optLine{int: penalty for a non-GT/AG chimeric junction} 
\optName{chimJunctionOverhangMin}
  \optValue{20}
  \optLine{int{\textgreater}=0: minimum overhang for a chimeric junction} 
\optName{chimSegmentReadGapMax}
  \optValue{0}
  \optLine{int{\textgreater}=0: maximum gap in the read sequence between chimeric segments} 
\optName{chimFilter}
  \optValue{banGenomicN}
  \optLine{string(s): different filters for chimeric alignments} 
\begin{optOptTable}
  \optOpt{None}   \optOptLine{no filtering}
  \optOpt{banGenomicN}   \optOptLine{Ns are not allowed in the genome sequence around the chimeric junction}
\end{optOptTable}
\end{optTable}
\optSection{Quantification of Annotations}\label{Quantification_of_Annotations}
\begin{optTable}
\optName{quantMode}
  \optValue{-}
  \optLine{string(s): types of quantification requested} 
\begin{optOptTable}
  \optOpt{-}   \optOptLine{none}
  \optOpt{TranscriptomeSAM}   \optOptLine{output SAM/BAM alignments to transcriptome into a separate file}
  \optOpt{GeneCounts}   \optOptLine{count reads per gene}
\end{optOptTable}
\optName{quantTranscriptomeBAMcompression}
  \optValue{1 1}
  \optLine{int: -1 to 10  transcriptome BAM compression level, -1=default compression (6?), 0=no compression, 10=maximum compression} 
\optName{quantTranscriptomeBan}
  \optValue{IndelSoftclipSingleend}
  \optLine{string: prohibit various alignment type} 
\begin{optOptTable}
  \optOpt{IndelSoftclipSingleend}   \optOptLine{prohibit indels, soft clipping and single-end alignments - compatible with RSEM}
  \optOpt{Singleend}   \optOptLine{prohibit single-end alignments}
\end{optOptTable}
\end{optTable}
\optSection{2-pass Mapping}\label{2-pass_Mapping}
\begin{optTable}
\optName{twopassMode}
  \optValue{None}
  \optLine{string: 2-pass mapping mode.} 
\begin{optOptTable}
  \optOpt{None}   \optOptLine{1-pass mapping}
  \optOpt{Basic}   \optOptLine{basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly}
\end{optOptTable}
\optName{twopass1readsN}
  \optValue{-1}
  \optLine{int: number of reads to process for the 1st step. Use very large number (or default -1) to map all reads in the first step.} 
\end{optTable}
