### versions versionSTAR 020201 int>0: STAR release numeric ID. Please do not change this value! versionGenome 020101 020200 int>0: oldest value of the Genome version compatible with this STAR release. Please do not change this value! ### PARAMETERS parametersFiles - string: name of a user-defined parameters file, "-": none. Can only be defined on the command line. ### RUN PARAMETERS runMode alignReads string: type of the run: alignReads ... map reads genomeGenerate ... generate genome files inputAlignmentsFromBAM ... input alignments from BAM. Presently only works with --outWigType to generate wiggle files. runThreadN 1 int: number of threads to run STAR ### GENOME PARAMETERS genomeDir ./GenomeDir/ string: path to the directory where genome files are stored (if runMode!=generateGenome) or will be generated (if runMode==generateGenome) genomeLoad NoSharedMemory mode of shared memory usage for the genome files string: LoadAndKeep ... load genome into shared and keep it in memory after run LoadAndRemove ... load genome into shared but remove it after run LoadAndExit ... load genome into shared memory and exit, keeping the genome in memory for future runs Remove ... do not map anything, just remove loaded genome from memory NoSharedMemory ... do not use shared memory, each job will have its own private copy of the genome ### GENOME GENERATION PARAMETERS genomeFastaFiles - fasta files with genomic sequence for genome files generation, only used if runMode==genomeGenerate string(s): path(s) to the files from the working directory (separated by spaces) genomeChrBinNbits 18 int: =log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins genomeSAindexNbases 14 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. genomeSAsparseD 1 int>0: suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction ### INPUT FROM BAM inputBAMfile - string: path to BAM input file, to be used with --runMode inputAlignmentsFromBAM ### READ PARAMETERS readFilesIn Read1 Read2 string(s): paths to files that contain input read1 (and, if needed, read2) readFilesCommand - 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 For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc. readMatesLengthsIn NotEqual string: Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same / not the same. NotEqual is safe in all situations. clip3pNbases 0 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. clip5pNbases 0 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. clip3pAdapterSeq - 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. clip3pAdapterMMp 0.1 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. clip3pAfterAdapterNbases 0 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. ### LIMITS limitGenomeGenerateRAM 31000000000 int>0: maximum available RAM (bytes) for genome generation limitIObufferSize 150000000 int>0: max available buffers size (bytes) for input/output, per thread limitOutSAMoneReadBytes 100000 int>0: max size of the SAM record for one read. Recommended value: >(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax limitOutSJoneRead 1000 int>0: max number of junctions for one read (including all multi-mappers) limitOutSJcollapsed 1000000 int>0: max number of collapsed junctions limitBAMsortRAM 0 int>=0: maximum available RAM for sorting BAM. If =0, it will be set to the genome index size ### OUTPUT: GENERAL outFileNamePrefix ./ string: output files name prefix (including full or relative path). Can only be defined on the command line. outTmpDir - string: path to a directory that will be used as temporary by STAR. All contents of this directory will be removed! - the temp directory will default to outFileNamePrefix_tmp outStd Log string: which output will be directed to stdout (standard out) Log : log messages SAM : alignments in SAM format (which normally are output to Aligned.out.sam file), normal standard output will go into Log.std.out BAM_Unsorted : alignments in BAM format, unsorted. Requires --outSAMtype BAM Unsorted BAM_SortedByCoordinate : alignments in BAM format, unsorted. Requires --outSAMtype BAM SortedByCoordinate BAM_Quant : alignments to transcriptome in BAM format, unsorted. Requires --quantMode TranscriptomeSAM outReadsUnmapped None string: output of unmapped reads (besides SAM) None : no output Fastx : output in separate fasta/fastq files, Unmapped.out.mate1/2 outQSconversionAdd 0 int: add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31) ### OUTPUT: SAM/BAM outSAMtype SAM strings: type of SAM/BAM output 1st word: BAM : output BAM without sorting SAM : output SAM without sorting None : no SAM/BAM output 2nd, 3rd ... Unsorted : standard unsorted SortedByCoordinate : sorted by coordinate outSAMmode Full string: mode of SAM output None : no SAM output Full : full SAM output NoQS : full SAM but without quality scores outSAMstrandField None string: Cufflinks-like strand field flag None : not used intronMotif : strand derived from the intron motif. Reads with inconsistent and/or non-canonical introns are filtered out. outSAMattributes Standard string: a string of desired SAM attributes, in the order desired for the output SAM NH HI AS nM NM MD jM jI XS Standard : NH HI AS nM All : NH HI AS nM NM MD jM jI None outSAMunmapped None string: output of unmapped reads in the SAM format None : no output Within : output unmapped reads within the main SAM file (i.e. Aligned.out.sam) outSAMorder Paired string: type of sorting for the SAM output Paired: one mate after the other for all paired alignments PairedKeepInputOrder: one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files outSAMprimaryFlag OneBestScore string: which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG OneBestScore : only one alignment with the best score is primary AllBestScore : all alignments with the best score are primary outSAMreadID Standard string: read ID record type Standard : first word (until space) from the FASTx read ID line, removing /1,/2 from the end Number : read number (index) in the FASTx file outSAMmapqUnique 255 int: 0 to 255: the MAPQ value for unique mappers outSAMattrRGline - 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". xxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted. Comma separated RG lines correspons to different (comma separated) input files in --readFilesIn. outSAMheaderHD - strings: @HD (header) line of the SAM header outSAMheaderPG - strings: extra @PG (software) line of the SAM header (in addition to STAR) outSAMheaderCommentFile - string: path to the file with @CO (comment) lines of the SAM header ### OUTPUT WIGGLE outWigType None string: type of sginal output None bedGraph outWigStrand Stranded string: strandedness of wigglle (bedGraph) output Stranded: separate strands, str1 and str2 Unstranded: collapsed strands None: no output outWigReferencesPrefix - string: prefix matching reference names to include in the output wiggle file, e.g. "chr.*" default: "-" - include all references ### OUTPUT FILTERING outFilterType Normal string: type of filtering Normal: standard filtering using only current alignment BySJout: keep only those reads that contain junctions that passed filtering into SJ.out.tab outFilterMultimapScoreRange 1 int: the score range below the maximum score for multimapping alignments outFilterMultimapNmax 10 int: read alignments will be output only if the read maps fewer than this value, otherwise no alignments will be output outFilterMismatchNmax 10 int: alignment will be output only if it has fewer mismatches than this value outFilterMismatchNoverLmax 0.3 int: alignment will be output only if its ratio of mismatches to *mapped* length is less than this value outFilterMismatchNoverReadLmax 1 int: alignment will be output only if its ratio of mismatches to *read* length is less than this value outFilterScoreMin 0 int: alignment will be output only if its score is higher than this value outFilterScoreMinOverLread 0.66 float: outFilterScoreMin normalized to read length (sum of mates' lengths for paired-end reads) outFilterMatchNmin 0 int: alignment will be output only if the number of matched bases is higher than this value outFilterMatchNminOverLread 0.66 float: outFilterMatchNmin normalized to read length (sum of mates' lengths for paired-end reads) outFilterIntronMotifs None string: filter alignment using their motifs None : no filtering RemoveNoncanonical : filter out alignments that contain non-canonical junctions RemoveNoncanonicalUnannotated : filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept. ### OUTPUT FILTERING: SPLICE JUNCTIONS outSJfilterReads All string: which reads to consider for collapsed splice junctions output All: all reads, unique- and multi-mappers Unique: uniquely mapping reads only outSJfilterOverhangMin 30 12 12 12 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 does not apply to annotated junctions outSJfilterCountUniqueMin 3 1 1 1 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 Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied does not apply to annotated junctions outSJfilterCountTotalMin 3 1 1 1 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 Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied does not apply to annotated junctions outSJfilterDistToOtherSJmin 10 0 5 10 4 integers>=0: minimum allowed distance to other junctions' donor/acceptor does not apply to annotated junctions outSJfilterIntronMaxVsReadN 50000 100000 200000 N integers>=0: maximum gap allowed for junctions supported by 1,2,3...N reads i.e. by default junctions supported by 1 read can have gaps <=50000b, by 2 reads: <=100000b, by 3 reads: <=200000. by >=4 reads any gap <=alignIntronMax does not apply to annotated junctions ### SCORING scoreGap 0 gap open penalty scoreGapNoncan -8 non-canonical gap open penalty (in addition to scoreGap) scoreGapGCAG -4 GC/AG and CT/GC gap open penalty (in addition to scoreGap) scoreGapATAC -8 AT/AC and GT/AT gap open penalty (in addition to scoreGap) scoreGenomicLengthLog2scale -0.25 extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength) scoreDelOpen -2 deletion open penalty scoreDelBase -2 deletion extension penalty per base (in addition to scoreDelOpen) scoreInsOpen -2 insertion open penalty scoreInsBase -2 insertion extension penalty per base (in addition to scoreInsOpen) scoreStitchSJshift 1 maximum score reduction while searching for SJ boundaries inthe stitching step ### ALIGNMENT and SEED PARAMETERS seedSearchStartLmax 50 int>0: defines the search start point through the read - the read is split into pieces no longer than this value seedSearchStartLmaxOverLread 1.0 float: seedSearchStartLmax normalized to read length (sum of mates' lengths for paired-end reads) seedSearchLmax 0 int>=0: defines the maximum length of the seeds, if =0 max seed lengthis infinite seedMultimapNmax 10000 int>0: only pieces that map fewer than this value are utilized in the stitching procedure seedPerReadNmax 1000 int>0: max number of seeds per read seedPerWindowNmax 50 int>0: max number of seeds per window seedNoneLociPerWindow 10 int>0: max number of one seed loci per window alignIntronMin 21 minimum intron size: genomic gap is considered intron if its length>=alignIntronMin, otherwise it is considered Deletion alignIntronMax 0 maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins alignMatesGapMax 0 maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins alignSJoverhangMin 5 int>0: minimum overhang (i.e. block size) for spliced alignments alignSJDBoverhangMin 3 int>0: minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments alignSplicedMateMapLmin 0 int>0: minimum mapped length for a read mate that is spliced alignSplicedMateMapLminOverLmate 0.66 float>0: alignSplicedMateMapLmin normalized to mate length alignWindowsPerReadNmax 10000 int>0: max number of windows per read alignTranscriptsPerWindowNmax 100 int>0: max number of transcripts per window alignTranscriptsPerReadNmax 10000 int>0: max number of different alignments per read to consider alignEndsType Local string: type of read ends alignment Local : standard local alignment with soft-clipping allowed EndToEnd: force end-to-end read alignment, do not soft-clip ### SPLICE JUNCTIONS DATABASE PARAMETERS sjdbFileChrStartEnd - string: path to the file with genomic coordinates (chr start end strand) for the introns sjdbGTFfile - string: path to the GTF file with annotations sjdbGTFchrPrefix - string: prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC geneomes) sjdbGTFfeatureExon exon string: feature type in GTF file to be used as exons for building transcripts sjdbGTFtagExonParentTranscript transcript_id string: tag name to be used as exons' parents for building transcripts sjdbOverhang 0 int>=0: length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1) if =0, splice junction database is not used sjdbScore 2 int: extra alignment score for alignmets that cross database junctions ### WINDOWS, ANCHORS, BINNING winAnchorMultimapNmax 50 int>0: max number of loci anchors are allowed to map to winBinNbits 16 int>0: =log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins. winAnchorDistNbins 9 int>0: max number of bins between two anchors that allows aggregation of anchors into one window winFlankNbins 4 int>0: log2(winFlank), where win Flank is the size of the left and right flanking regions for each window ### CHIMERIC ALIGNMENTS chimSegmentMin 0 int>=0: minimum length of chimeric segment length, if ==0, no chimeric output chimScoreMin 0 int>=0: minimum total (summed) score of the chimeric segments chimScoreDropMax 20 int>=0: max drop (difference) of chimeric score (the sum of scores of all chimeric segements) from the read length chimScoreSeparation 10 int>=0: minimum difference (separation) between the best chimeric score and the next one chimScoreJunctionNonGTAG -1 int: penalty for a non-GT/AG chimeric junction chimJunctionOverhangMin 20 int>=0: minimum overhang for a chimeric junction ### QUANTIFICATION OF ANNOTATIONS quantMode - string(s): types of qunatification requested - : None TranscriptomeSAM : output SAM/BAM alignments to transcriptome into a separate file ### NOT USED Smith-Waterman alignment parameters for PacBio reads swMode 0 int>=0: 0: no SW alignments, 1: full SW alignment swWinCoverageMinP 50 int>0: minimum read coverage percentage in a window that will be aligned with SW