|
18 | 18 | \optName{runMode} |
19 | 19 | \optValue{alignReads} |
20 | 20 | \optLine{string: type of the run.} |
| 21 | +\begin{optOptTable} |
| 22 | + \optOpt{alignReads} \optOptLine{map reads} |
| 23 | + \optOpt{genomeGenerate} \optOptLine{generate genome files} |
| 24 | + \optOpt{inputAlignmentsFromBAM} \optOptLine{input alignments from BAM. Presently only works with --outWigType and --bamRemoveDuplicates options.} |
| 25 | + \optOpt{liftOver} \optOptLine{lift-over of GTF files (--sjdbGTFfile) between genome assemblies using chain file(s) from --genomeChainFiles.} |
| 26 | + \optOpt{soloCellFiltering {\textless}/path/to/raw/count/dir/{\textgreater} {\textless}/path/to/output/prefix{\textgreater}} \optOptLine{STARsolo cell filtering ("calling") without remapping, followed by the path to raw count directory and output (filtered) prefix} |
| 27 | +\end{optOptTable} |
21 | 28 | \optName{runThreadN} |
22 | 29 | \optValue{1} |
23 | 30 | \optLine{int: number of threads to run STAR} |
|
357 | 364 | \optLine{***STARsolo:} |
358 | 365 | \begin{optOptTable} |
359 | 366 | \optOpt{CR CY UR UY} \optOptLine{sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing.} |
360 | | - \optOpt{GX GN} \optOptLine{gene ID and gene name.} |
| 367 | + \optOpt{GX GN} \optOptLine{gene ID and gene name for unique-gene reads.} |
| 368 | + \optOpt{gx gn} \optOptLine{gene IDs and gene names for unique- and multi-gene reads.} |
361 | 369 | \optOpt{CB UB} \optOptLine{error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --outSAMtype BAM SortedByCoordinate.} |
362 | 370 | \optOpt{sM} \optOptLine{assessment of CB and UMI.} |
363 | 371 | \optOpt{sS} \optOptLine{sequence of the entire barcode (CB,UMI,adapter).} |
|
879 | 887 | \optLine{string(s): type of single-cell RNA-seq} |
880 | 888 | \begin{optOptTable} |
881 | 889 | \optOpt{CB{\textunderscore}UMI{\textunderscore}Simple} \optOptLine{(a.k.a. Droplet) one UMI and one Cell Barcode of fixed length in read2, e.g. Drop-seq and 10X Chromium.} |
882 | | - \optOpt{CB{\textunderscore}UMI{\textunderscore}Complex} \optOptLine{one UMI of fixed length, but multiple Cell Barcodes of varying length, as well as adapters sequences are allowed in read2 only, e.g. inDrop.} |
| 890 | + \optOpt{CB{\textunderscore}UMI{\textunderscore}Complex} \optOptLine{multiple Cell Barcodes of varying length, one UMI of fixed length and one adapter sequence of fixed length are allowed in read2 only (e.g. inDrop, ddSeq).} |
883 | 891 | \optOpt{CB{\textunderscore}samTagOut} \optOptLine{output Cell Barcode as CR and/or CB SAm tag. No UMI counting. --readFilesIn cDNA{\textunderscore}read1 [cDNA{\textunderscore}read2 if paired-end] CellBarcode{\textunderscore}read . Requires --outSAMtype BAM Unsorted [and/or SortedByCoordinate]} |
884 | 892 | \optOpt{SmartSeq} \optOptLine{Smart-seq: each cell in a separate FASTQ (paired- or single-end), barcodes are corresponding read-groups, no UMI sequences, alignments deduplicated according to alignment start and end (after extending soft-clipped bases)} |
885 | 893 | \end{optOptTable} |
|
933 | 941 | \optLine{--soloCBposition 3{\textunderscore}9{\textunderscore}3{\textunderscore}14} |
934 | 942 | \optName{soloAdapterSequence} |
935 | 943 | \optValue{-} |
936 | | - \optLine{string: adapter sequence to anchor barcodes.} |
| 944 | + \optLine{string: adapter sequence to anchor barcodes. Only one adapter sequence is allowed.} |
937 | 945 | \optName{soloAdapterMismatchesNmax} |
938 | 946 | \optValue{1} |
939 | 947 | \optLine{int{\textgreater}0: maximum number of mismatches allowed in adapter sequence.} |
|
949 | 957 | \begin{optOptTable} |
950 | 958 | \optOpt{1MM{\textunderscore}multi{\textunderscore}pseudocounts} \optOptLine{same as 1MM{\textunderscore}Multi, but pseudocounts of 1 are added to all whitelist barcodes.} |
951 | 959 | \optOpt{1MM{\textunderscore}multi{\textunderscore}Nbase{\textunderscore}pseudocounts} \optOptLine{same as 1MM{\textunderscore}multi{\textunderscore}pseudocounts, multimatching to WL is allowed for CBs with N-bases. This option matches best with CellRanger {\textgreater}= 3.0.0} |
| 960 | + \optOpt{ParseBio{\textunderscore}ED3} \optOptLine{allow up to edit distance of 3 fpr each of the barcodes. May include one deletion + one insertion. Only works with --soloType CB{\textunderscore}UMI{\textunderscore}Complex. Matches to multiple passlist barcdoes are not allowed. Similar to ParseBio Split-seq pipeline.} |
952 | 961 | \end{optOptTable} |
953 | 962 | \optName{soloInputSAMattrBarcodeSeq} |
954 | 963 | \optValue{-} |
|
974 | 983 | \begin{optOptTable} |
975 | 984 | \optOpt{Gene} \optOptLine{genes: reads match the gene transcript} |
976 | 985 | \optOpt{SJ} \optOptLine{splice junctions: reported in SJ.out.tab} |
977 | | - \optOpt{GeneFull} \optOptLine{full genes: count all reads overlapping genes' exons and introns} |
| 986 | + \optOpt{GeneFull} \optOptLine{full gene (pre-mRNA): count all reads overlapping genes' exons and introns} |
| 987 | + \optOpt{GeneFull{\textunderscore}ExonOverIntron} \optOptLine{full gene (pre-mRNA): count all reads overlapping genes' exons and introns: prioritize 100% overlap with exons} |
| 988 | + \optOpt{GeneFull{\textunderscore}Ex50pAS} \optOptLine{full gene (pre-RNA): count all reads overlapping genes' exons and introns: prioritize {\textgreater}50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.} |
978 | 989 | \end{optOptTable} |
979 | 990 | \optName{soloMultiMappers} |
980 | 991 | \optValue{Unique} |
981 | 992 | \optLine{string(s): counting method for reads mapping to multiple genes } |
982 | 993 | \begin{optOptTable} |
983 | 994 | \optOpt{Unique} \optOptLine{count only reads that map to unique genes} |
984 | 995 | \optOpt{Uniform} \optOptLine{uniformly distribute multi-genic UMIs to all genes} |
985 | | - \optOpt{Rescue} \optOptLine{distribute UMIs proportionally to unique+uniform counts (~ first iteartion of EM)} |
| 996 | + \optOpt{Rescue} \optOptLine{distribute UMIs proportionally to unique+uniform counts (~ first iteration of EM)} |
986 | 997 | \optOpt{PropUnique} \optOptLine{distribute UMIs proportionally to unique mappers, if present, and uniformly if not.} |
| 998 | + \optOpt{EM} \optOptLine{multi-gene UMIs are distributed using Expectation Maximization algorithm} |
987 | 999 | \end{optOptTable} |
988 | 1000 | \optName{soloUMIdedup} |
989 | 1001 | \optValue{1MM{\textunderscore}All} |
|
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