RNA

Path to the pair ended fastq files. Files can be in fastq or fastq.gz format or a google cloud storage object.

e.g. '--in-fq sampleX_1_1.fastq.gz sampleX_1_2.fastq.gz' (default: None)

Path to a genome resource library directory. We assume that the indexing required to run star has been completed by the user. (default: None)

Path to the directory that will contain all of the generated files (default: None)

Number of running worker threads per GPU (default: 4)

2-pass mapping mode. The string can be “None” for 1-pass mapping or “Basic” for basic 2-pass mapping with all 1st pass junctions inserted into the genome indices on the fly (default: None)

Length (bases) of the SA pre-indexing string. Longer strings will use much more memory, but allow for faster searches. A value between 10 and 15 is recommended. For small genomes, the parameter must be scaled down to min(14, log2(GenomeLength)/2 - 1) (default: 14)

Maximum align intron size. If this value is 0, the maximum size will be determined by (2^winBinNbits)*winAnchorDistNbins (default: 0)

Minimum align intron size. Genomic gap is considered intron if its length is greater than or equal to this value, otherwise it is considered Deletion (default: 21)

Minimum number of matched bases required for alignment output (default: 0)

Same as –min-match-filter, but normalized to the read length (sum of mates’ lengths for paired-end reads) (default: 0.66)

Type of filter alignment using their motifs. This string can be “None” for no filtering, “RemoveNoncanonical” for filtering out alignments that contain non-canonical junctions, or “RemoveNoncanonicalUnannotated” for filtering out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept (default: None)

Maximum number of mismatches allowed for an alignment to be output (default: 10)

Maximum ratio of mismatches to mapped length allowed for an alignment to be output (default: 0.3)

Maximum number of loci the read is allowed to map to for all alignments to be output. Otherwise, no alignments will be output and the read will be counted as “mapped to too many loci” in the Log.final.out (default: 10)

Type of output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s). This string can be “None” for no output or “Fastx” for output in separate fasta/fastq files, Unmapped.out.mate1/2 (default: None)

Type of output of unmapped reads in the SAM format. The string can be “None” for no output, “Within” to output unmapped reads within the main SAM file, “KeepPairs” for no output and unmapped mates will be recorded for each alignment, or “Within_KeepPairs” to output unmapped reads within the main SAM file and unmapped mates will be recorded for each alignment (default: None)

SAM/BAM read group line. The first word contains the read group identifier and must start with “ID:”,

e.g. --out-sam-rg-line '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 correspond to different input read files. Commas have to be surrounded by spaces,

e.g. '--out-sam-rg-line 'ID:xxx , ID:zzz "DS:z z" , ID:yyy DS:yyyy’

(default: None)

A string of SAM attributes in the order desired for the output SAM. The string can contain any combination of the following attributes: {NH, HI, AS, nM, NM, MD, jM, jI, XS, MC, ch}. Alternatively, the string can be “None” for no attributes, “Standard” for the attributes {NH, HI, AS, nM}, or “All” for the attributes {NH, HI, AS, nM, NM, MD, jM, jI, MC, ch}.

e.g. --outSAMattributes NH nM jI XS ch

(default: Standard)

Cufflinks-like strand field flag. The string can be “None” for no flag or “intronMotif” for the strand derived from the intron motif. Reads with inconsistent and/or non-canonical introns will be filtered out (default: None)

SAM output mode. The string can be “None” for no SAM output, “Full” for full SAM output, or “NoQS” for full SAM output without quality scores (default: Full)

The MAPQ value for unique mappers. Must be in the range [0, 255] (default: 255)

Command line to execute for each of the input files. 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. (default: None)

Minimum score required for alignment output, normalized to the read length (sum of mates’ lengths for paired-end reads) (default: 0.66)

Minimum mapped length for a read mate that is spliced, normalized to the mate length. Must be greater than 0 (default: 0.66)

Maximum number of mismatches for stitching of the splice junctions. A limit must be specified for each of the following: (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. To indicate no limit for any of the four options, use -1 (default: [0, -1, 0, 0])

Maximum size of the SAM record (bytes) for one read. Recommended value: >(2*(LengthMate1+LengthMate2+100)*o utFilterMultimapNmax. Must be greater than 0 (default: 100000)

Maximum number of different alignments per read to consider. Must be greater than 0 (default: 10000)

Splice junction penalty (independent on intron motif) (default: 0)

Defines the search start point through the read. The read split pieces will not be longer than this value. Must be greater than 0 (default: 50)

Maximum available RAM (bytes) for sorting BAM. If this value is 0, it will be set to the genome index size. Must be greater than or equal to 0 (default: 0)

Type of read ends alignment. Can be one of two options: “Local” will do a standard local alignment with soft-clipping allowed; “EndToEnd” will force an end-to-end read alignment with no soft-clipping (default: Local)

How to flush ambiguous insertion positions. The string can be “None” to not flush insertions or “Right” to flush insertions to the right (default: None)

Maximum gap between two mates. If 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins (default: 0)

Minimum mapped length for a read mate that is spliced. Must be greater than 0 (default: 0)

Maximum number of collapsed junctions. Must be greater than 0 (default: 1000000)

Minimum overhang (i.e. block size) for spliced alignments. Must be greater than 0 (default: 5)

Minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments. Must be greater than 0 (default: 3)

Length of the donor/acceptor sequence on each side of the junctions. Ideally this value should be equal to mate_length - 1. Must be greater than 0 (default: 100)

Minimum overhang for the Chimeric.out.junction file. Must be greater than or equal to 0 (default: 20)

Minimum chimeric segment length. If it is set to 0, there will be no chimeric output. Must be greater than or equal to 0 (default: 0)

Maximum number of chimeric multi-alignments. If it is set to 0, the old scheme for chimeric detection which only considered unique alignments will be used. Must be greater than or equal to 0 (default: 0)

The score range for multi-mapping chimeras below the best chimeric score. This option only works with –max-chim-multimap > 1. Must be greater than or equal to 0 (default: 1)

The penalty for a non-GT/AG chimeric junction (default: -1)

To trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be smaller than this value. Must be greater than or equal to 0 (default: 20)

Formatting type for the Chimeric.out.junction file. Possible types are {0, 1}. If type 0, there will be no comment lines/headers. If type 1, there will be comment lines at the end of the file: command line and Nreads: total, unique, multi (default: 0)

Type of chimeric output. This string can be “Junctions” for Chimeric.out.junction, “WithinBAM” for main aligned BAM files (Aligned.*.bam), “WithinBAM_HardClip” for hard-clipping in the CIGAR for supplemental chimeric alignments, or “WithinBAM_SoftClip” for soft-clipping in the CIGAR for supplemental chimeric alignments (default: Junctions)

Prefix filename for output data (default: None)

Number of GPUs to use for a run (default: 1)

Which GPU devices to use for a run. By default, all GPU devices will be used. To set specific GPU devices, enter a comma-separated list of GPU device numbers.

Path to the Chimeric.out.junction file produced by STAR (default: None)

Path to a genome resource library directory. For more information, visit https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion#data_resources_required

Path to the directory that will contain all of the generated files (default: None)

Number of threads for worker (default: 4)