|
66 | 66 | \optLine{uint(s){\textgreater}0: genome files exact sizes in bytes. Typically, this should not be defined by the user.} |
67 | 67 | \optName{genomeTransformOutput} |
68 | 68 | \optValue{None} |
69 | | - \optLine{string(s) which output to transform back to original genome} |
| 69 | + \optLine{string(s): which output to transform back to original genome} |
70 | 70 | \begin{optOptTable} |
71 | 71 | \optOpt{SAM} \optOptLine{SAM/BAM alignments} |
72 | 72 | \optOpt{SJ} \optOptLine{splice junctions (SJ.out.tab)} |
|
75 | 75 | \end{optOptTable} |
76 | 76 | \optName{genomeChrSetMitochondrial} |
77 | 77 | \optValue{chrM M MT} |
78 | | - \optLine{string(s) names of the mitochondrial chromosomes. Presently only used for STARsolo statisics output/} |
| 78 | + \optLine{string(s): names of the mitochondrial chromosomes. Presently only used for STARsolo statistics output/} |
79 | 79 | \end{optTable} |
80 | 80 | \optSection{Genome Indexing Parameters - only used with --runMode genomeGenerate}\label{Genome_Indexing_Parameters_-_only_used_with_--runMode_genomeGenerate} |
81 | 81 | \begin{optTable} |
|
107 | 107 | \begin{optTable} |
108 | 108 | \optName{sjdbFileChrStartEnd} |
109 | 109 | \optValue{-} |
110 | | - \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.} |
| 110 | + \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 and will be concatenated.} |
111 | 111 | \optName{sjdbGTFfile} |
112 | 112 | \optValue{-} |
113 | 113 | \optLine{string: path to the GTF file with annotations} |
|
125 | 125 | \optLine{string: GTF attribute name for parent gene ID (default "gene{\textunderscore}id" works for GTF files)} |
126 | 126 | \optName{sjdbGTFtagExonParentGeneName} |
127 | 127 | \optValue{gene{\textunderscore}name} |
128 | | - \optLine{string(s): GTF attrbute name for parent gene name} |
| 128 | + \optLine{string(s): GTF attribute name for parent gene name} |
129 | 129 | \optName{sjdbGTFtagExonParentGeneType} |
130 | 130 | \optValue{gene{\textunderscore}type gene{\textunderscore}biotype} |
131 | | - \optLine{string(s): GTF attrbute name for parent gene type} |
| 131 | + \optLine{string(s): GTF attribute name for parent gene type} |
132 | 132 | \optName{sjdbOverhang} |
133 | 133 | \optValue{100} |
134 | 134 | \optLine{int{\textgreater}0: length of the donor/acceptor sequence on each side of the junctions, ideally = (mate{\textunderscore}length - 1)} |
|
240 | 240 | \optLine{int{\textgreater}0: maximum available RAM (bytes) for genome generation} |
241 | 241 | \optName{limitIObufferSize} |
242 | 242 | \optValue{30000000 50000000} |
243 | | - \optLine{int{\textgreater}0: max available buffers size (bytes) for input/output, per thread} |
| 243 | + \optLine{int(s){\textgreater}0: max available buffers size (bytes) for input/output, per thread} |
244 | 244 | \optName{limitOutSAMoneReadBytes} |
245 | 245 | \optValue{100000} |
246 | 246 | \optLine{int{\textgreater}0: max size of the SAM record (bytes) for one read. Recommended value: {\textgreater}(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax} |
|
255 | 255 | \optLine{int{\textgreater}=0: maximum available RAM (bytes) for sorting BAM. If =0, it will be set to the genome index size. 0 value can only be used with --genomeLoad NoSharedMemory option.} |
256 | 256 | \optName{limitSjdbInsertNsj} |
257 | 257 | \optValue{1000000} |
258 | | - \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} |
| 258 | + \optLine{int{\textgreater}=0: maximum number of junctions 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} |
259 | 259 | \optName{limitNreadsSoft} |
260 | 260 | \optValue{-1} |
261 | 261 | \optLine{int: soft limit on the number of reads} |
|
268 | 268 | \optName{outTmpDir} |
269 | 269 | \optValue{-} |
270 | 270 | \optLine{string: path to a directory that will be used as temporary by STAR. All contents of this directory will be removed!} |
271 | | - \optLine{- the temp directory will default to outFileNamePrefix{\textunderscore}STARtmp} |
| 271 | +\begin{optOptTable} |
| 272 | + \optOpt{-} \optOptLine{the temp directory will default to outFileNamePrefix{\textunderscore}STARtmp} |
| 273 | +\end{optOptTable} |
272 | 274 | \optName{outTmpKeep} |
273 | 275 | \optValue{None} |
274 | | - \optLine{string: whether to keep the tempporary files after STAR runs is finished} |
| 276 | + \optLine{string: whether to keep the temporary files after STAR runs is finished} |
275 | 277 | \begin{optOptTable} |
276 | 278 | \optOpt{None} \optOptLine{remove all temporary files} |
| 279 | + \optOpt{All} \optOptLine{keep all files} |
277 | 280 | \end{optOptTable} |
278 | | - \optLine{All .. keep all files} |
279 | 281 | \optName{outStd} |
280 | 282 | \optValue{Log} |
281 | 283 | \optLine{string: which output will be directed to stdout (standard out)} |
|
337 | 339 | \end{optOptTable} |
338 | 340 | \optName{outSAMattributes} |
339 | 341 | \optValue{Standard} |
340 | | - \optLine{string: a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order.} |
| 342 | + \optLine{string(s): a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order.} |
341 | 343 | \optLine{***Presets:} |
342 | 344 | \begin{optOptTable} |
343 | 345 | \optOpt{None} \optOptLine{no attributes} |
|
468 | 470 | \optLine{int: {\textgreater}=0: number of threads for BAM sorting. 0 will default to min(6,--runThreadN).} |
469 | 471 | \optName{outBAMsortingBinsN} |
470 | 472 | \optValue{50} |
471 | | - \optLine{int: {\textgreater}0: number of genome bins fo coordinate-sorting} |
| 473 | + \optLine{int: {\textgreater}0: number of genome bins for coordinate-sorting} |
472 | 474 | \end{optTable} |
473 | 475 | \optSection{BAM processing}\label{BAM_processing} |
474 | 476 | \begin{optTable} |
|
548 | 550 | \optLine{int: alignment will be output only if its score is higher than or equal to this value.} |
549 | 551 | \optName{outFilterScoreMinOverLread} |
550 | 552 | \optValue{0.66} |
551 | | - \optLine{real: same as outFilterScoreMin, but normalized to read length (sum of mates' lengths for paired-end reads)} |
| 553 | + \optLine{real: same as outFilterScoreMin, but normalized to read length (sum of mates' lengths for paired-end reads)} |
552 | 554 | \optName{outFilterMatchNmin} |
553 | 555 | \optValue{0} |
554 | 556 | \optLine{int: alignment will be output only if the number of matched bases is higher than or equal to this value.} |
|
624 | 626 | \optLine{int: non-canonical junction penalty (in addition to scoreGap)} |
625 | 627 | \optName{scoreGapGCAG} |
626 | 628 | \optValue{-4} |
627 | | - \optLine{GC/AG and CT/GC junction penalty (in addition to scoreGap)} |
| 629 | + \optLine{int: GC/AG and CT/GC junction penalty (in addition to scoreGap)} |
628 | 630 | \optName{scoreGapATAC} |
629 | 631 | \optValue{-8} |
630 | | - \optLine{AT/AC and GT/AT junction penalty (in addition to scoreGap)} |
| 632 | + \optLine{int: AT/AC and GT/AT junction penalty (in addition to scoreGap)} |
631 | 633 | \optName{scoreGenomicLengthLog2scale} |
632 | 634 | \optValue{-0.25} |
633 | | - \optLine{extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)} |
| 635 | + \optLine{int: extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)} |
634 | 636 | \optName{scoreDelOpen} |
635 | 637 | \optValue{-2} |
636 | | - \optLine{deletion open penalty} |
| 638 | + \optLine{int: deletion open penalty} |
637 | 639 | \optName{scoreDelBase} |
638 | 640 | \optValue{-2} |
639 | | - \optLine{deletion extension penalty per base (in addition to scoreDelOpen)} |
| 641 | + \optLine{int: deletion extension penalty per base (in addition to scoreDelOpen)} |
640 | 642 | \optName{scoreInsOpen} |
641 | 643 | \optValue{-2} |
642 | | - \optLine{insertion open penalty} |
| 644 | + \optLine{int: insertion open penalty} |
643 | 645 | \optName{scoreInsBase} |
644 | 646 | \optValue{-2} |
645 | | - \optLine{insertion extension penalty per base (in addition to scoreInsOpen)} |
| 647 | + \optLine{int: insertion extension penalty per base (in addition to scoreInsOpen)} |
646 | 648 | \optName{scoreStitchSJshift} |
647 | 649 | \optValue{1} |
648 | | - \optLine{maximum score reduction while searching for SJ boundaries in the stitching step} |
| 650 | + \optLine{int: maximum score reduction while searching for SJ boundaries in the stitching step} |
649 | 651 | \end{optTable} |
650 | 652 | \optSection{Alignments and Seeding}\label{Alignments_and_Seeding} |
651 | 653 | \begin{optTable} |
|
678 | 680 | \optLine{int{\textgreater}0: min length of seeds to be mapped} |
679 | 681 | \optName{alignIntronMin} |
680 | 682 | \optValue{21} |
681 | | - \optLine{minimum intron size: genomic gap is considered intron if its length{\textgreater}=alignIntronMin, otherwise it is considered Deletion} |
| 683 | + \optLine{int: minimum intron size, genomic gap is considered intron if its length{\textgreater}=alignIntronMin, otherwise it is considered Deletion} |
682 | 684 | \optName{alignIntronMax} |
683 | 685 | \optValue{0} |
684 | | - \optLine{maximum intron size, if 0, max intron size will be determined by (2\^{}winBinNbits)*winAnchorDistNbins} |
| 686 | + \optLine{int: maximum intron size, if 0, max intron size will be determined by (2\^{}winBinNbits)*winAnchorDistNbins} |
685 | 687 | \optName{alignMatesGapMax} |
686 | 688 | \optValue{0} |
687 | | - \optLine{maximum gap between two mates, if 0, max intron gap will be determined by (2\^{}winBinNbits)*winAnchorDistNbins} |
| 689 | + \optLine{int: maximum gap between two mates, if 0, max intron gap will be determined by (2\^{}winBinNbits)*winAnchorDistNbins} |
688 | 690 | \optName{alignSJoverhangMin} |
689 | 691 | \optValue{5} |
690 | 692 | \optLine{int{\textgreater}0: minimum overhang (i.e. block size) for spliced alignments} |
|
747 | 749 | \begin{optTable} |
748 | 750 | \optName{peOverlapNbasesMin} |
749 | 751 | \optValue{0} |
750 | | - \optLine{int{\textgreater}=0: minimum number of overlap bases to trigger mates merging and realignment. Specify {\textgreater}0 value to switch on the "merginf of overlapping mates" algorithm.} |
| 752 | + \optLine{int{\textgreater}=0: minimum number of overlapping bases to trigger mates merging and realignment. Specify {\textgreater}0 value to switch on the "merginf of overlapping mates" algorithm.} |
751 | 753 | \optName{peOverlapMMp} |
752 | 754 | \optValue{0.01} |
753 | 755 | \optLine{real, {\textgreater}=0 {\&} {\textless}1: maximum proportion of mismatched bases in the overlap area} |
|
847 | 849 | \optOpt{GeneCounts} \optOptLine{count reads per gene} |
848 | 850 | \end{optOptTable} |
849 | 851 | \optName{quantTranscriptomeBAMcompression} |
850 | | - \optValue{1 1} |
| 852 | + \optValue{1} |
851 | 853 | \optLine{int: -2 to 10 transcriptome BAM compression level} |
852 | 854 | \begin{optOptTable} |
853 | 855 | \optOpt{-2} \optOptLine{no BAM output} |
854 | 856 | \optOpt{-1} \optOptLine{default compression (6?)} |
855 | 857 | \optOpt{0} \optOptLine{no compression} |
856 | 858 | \optOpt{10} \optOptLine{maximum compression} |
857 | 859 | \end{optOptTable} |
858 | | -\optName{quantTranscriptomeBan} |
859 | | - \optValue{IndelSoftclipSingleend} |
860 | | - \optLine{string: prohibit various alignment type} |
| 860 | +\optName{quantTranscriptomeSAMoutput} |
| 861 | + \optValue{BanSingleEnd{\textunderscore}BanIndels{\textunderscore}ExtendSoftclip} |
| 862 | + \optLine{string: alignment filtering for TranscriptomeSAM output} |
861 | 863 | \begin{optOptTable} |
862 | | - \optOpt{IndelSoftclipSingleend} \optOptLine{prohibit indels, soft clipping and single-end alignments - compatible with RSEM} |
863 | | - \optOpt{Singleend} \optOptLine{prohibit single-end alignments} |
| 864 | + \optOpt{BanSingleEnd{\textunderscore}BanIndels{\textunderscore}ExtendSoftclip} \optOptLine{prohibit indels and single-end alignments, extend softclips - compatible with RSEM} |
| 865 | + \optOpt{BanSingleEnd} \optOptLine{prohibit single-end alignments, allow indels and softclips} |
| 866 | + \optOpt{BanSingleEnd{\textunderscore}ExtendSoftclip} \optOptLine{prohibit single-end alignments, extend softclips, allow indels} |
864 | 867 | \end{optOptTable} |
865 | 868 | \end{optTable} |
866 | 869 | \optSection{2-pass Mapping}\label{2-pass_Mapping} |
|
936 | 939 | \end{optOptTable} |
937 | 940 | \optName{soloCBposition} |
938 | 941 | \optValue{-} |
939 | | - \optLine{strings(s) position of Cell Barcode(s) on the barcode read.} |
| 942 | + \optLine{strings(s): position of Cell Barcode(s) on the barcode read.} |
940 | 943 | \optLine{Presently only works with --soloType CB{\textunderscore}UMI{\textunderscore}Complex, and barcodes are assumed to be on Read2.} |
941 | 944 | \optLine{Format for each barcode: startAnchor{\textunderscore}startPosition{\textunderscore}endAnchor{\textunderscore}endPosition} |
942 | 945 | \optLine{start(end)Anchor defines the Anchor Base for the CB: 0: read start; 1: read end; 2: adapter start; 3: adapter end} |
|
946 | 949 | \optLine{--soloCBposition 0{\textunderscore}0{\textunderscore}2{\textunderscore}-1 3{\textunderscore}1{\textunderscore}3{\textunderscore}8} |
947 | 950 | \optName{soloUMIposition} |
948 | 951 | \optValue{-} |
949 | | - \optLine{string position of the UMI on the barcode read, same as soloCBposition} |
| 952 | + \optLine{string: position of the UMI on the barcode read, same as soloCBposition} |
950 | 953 | \optLine{Example: inDrop (Zilionis et al, Nat. Protocols, 2017):} |
951 | 954 | \optLine{--soloCBposition 3{\textunderscore}9{\textunderscore}3{\textunderscore}14} |
952 | 955 | \optName{soloAdapterSequence} |
|
1020 | 1023 | \end{optOptTable} |
1021 | 1024 | \optName{soloUMIfiltering} |
1022 | 1025 | \optValue{-} |
1023 | | - \optLine{string(s) type of UMI filtering (for reads uniquely mapping to genes)} |
| 1026 | + \optLine{string(s): type of UMI filtering (for reads uniquely mapping to genes)} |
1024 | 1027 | \begin{optOptTable} |
1025 | 1028 | \optOpt{-} \optOptLine{basic filtering: remove UMIs with N and homopolymers (similar to CellRanger 2.2.0).} |
1026 | 1029 | \optOpt{MultiGeneUMI} \optOptLine{basic + remove lower-count UMIs that map to more than one gene.} |
|
1030 | 1033 | \optLine{Only works with --soloUMIdedup 1MM{\textunderscore}CR} |
1031 | 1034 | \optName{soloOutFileNames} |
1032 | 1035 | \optValue{Solo.out/ features.tsv barcodes.tsv matrix.mtx} |
1033 | | - \optLine{string(s) file names for STARsolo output:} |
| 1036 | + \optLine{string(s): file names for STARsolo output:} |
1034 | 1037 | \optLine{file{\textunderscore}name{\textunderscore}prefix gene{\textunderscore}names barcode{\textunderscore}sequences cell{\textunderscore}feature{\textunderscore}count{\textunderscore}matrix} |
1035 | 1038 | \optName{soloCellFilter} |
1036 | 1039 | \optValue{CellRanger2.2 3000 0.99 10} |
|
0 commit comments