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STAR is an aligner for RNA sequencing. It rapidly aligns RNA-seq reads against a genome index. For more information, see the tool's GitHub repo and manual.

Function Call


Function Arguments

See the Notes section below for more details.

Argument Use in place of: Description
read_one --readFilesIn Paths to single-end read input file, or R1 of paired-end read input files. The files can be a local or remote, see Using Files.
read_two --readFilesIn (optional) Path to read 2 of paired-end read input files. This can be a local filepath or an AWS S3 URI.
output_path --outFileNamePrefix (optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Using Files.
tool_args all other arguments (optional) Additional arguments to be passed to STAR. This should be a string of arguments like the command line. See Supported Additional Arguments for more details.
database_name --genomeDir* (optional) Name of database to use for STAR alignment. Defaults to "GRCh38" (human genome).
database_version --genomeDir* (optional) Version of database to use for STAR alignment. Defaults to "1".
is_async Whether to run a job asynchronously. See Async Runs for more.

See the Databases section for more details.


Single-end and paired-end inputs

Paired-end read inputs should be specified with both read_one and read_two.

For single-end read inputs, specify the input as read_one argument and omit read_two.

Tool Versions

Toolchest currently supports version 2.7.9a of STAR. Every request to run STAR with Toolchest will default to this version.


Toolchest currently supports the following databases for STAR:

database_name database_version Description
GRCh38 1 GRCh38 (human) genome, built from patch GRCh38.p13 using STAR 2.7.4a

Supported Additional Arguments

  • --alignEndsProtrude
  • --alignEndsType
  • --alignInsertionFlush
  • --alignIntronMax
  • --alignIntronMin
  • --alignMatesGapMax
  • --alignSJDBoverhangMin
  • --alignSJoverhangMin
  • --alignSJstitchMismatchNmax
  • --alignSoftClipAtReferenceEnds
  • --alignSplicedMateMapLmin
  • --alignSplicedMateMapLminOverLmate
  • --alignTranscriptsPerReadNmax
  • --alignTranscriptsPerWindowNmax
  • --alignWindowsPerReadNmax
  • --outFilterMatchNmin
  • --outFilterMismatchNmax
  • --outFilterMismatchNoverReadLmax
  • --outFilterMultimapNmax
  • --outFilterType
  • --outReadsUnmapped
  • --outSAMstrandField
  • --outSAMtype
  • --quantMode
  • --quantTranscriptomeBAMcompression
  • --quantTranscriptomeBan
  • --readFilesCommand
  • --readFilesType
  • --readMapNumber
  • --readMatesLengthsIn
  • --readStrand
  • --runRNGseed
  • --scoreDelBase
  • --scoreDelOpen
  • --scoreGap
  • --scoreGapATAC
  • --scoreGapGCAG
  • --scoreGapNoncan
  • --scoreGenomicLengthLog2scale
  • --scoreInsBase
  • --scoreInsOpen
  • --scoreStitchSJshift
  • --seedMultimapNmax
  • --seedNoneLociPerWindow
  • --seedPerReadNmax
  • --seedPerWindowNmax
  • --seedSearchLmax
  • --seedSearchStartLmax
  • --seedSearchStartLmaxOverLread
  • --seedSplitMin
  • --sjdbInsertSave
  • --twopassMode
  • --winAnchorDistNbins
  • --winAnchorMultimapNmax
  • --winBinNbits
  • --winFlankNbins
  • --winReadCoverageBasesMin
  • --winReadCoverageRelativeMin

Additional arguments can be specified under the tool_args argument.