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

toolchest.STAR(
    read_one,
    read_two=None,
    output_path=None,
    tool_args="",
    database_name="GRCh38",
    database_version="1",
    is_async=False,
)
toolchest$STAR(
    read_one,
    read_two = NULL,
    output_path = NULL,
    tool_args = "",
    database_name = "GRCh38",
    database_version = "1",
    is_async = FALSE
)

Function Arguments

See the Notes section below for more details.

Argument

Use in place of:

Description

read_one

--readFilesIn

Path to single-end read input file or read 1 of paired-end read input files. This can be a local filepath or an AWS S3 URI.

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 to a local directory where the output files will be downloaded.
If omitted, skips download. The outputs can be downloaded manually.

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 the Databases section for more details.

Return Value

This function call returns a Toolchest output object, which contains the run ID and locations of downloaded output files. See Output Objects for more details.

Notes

Amazon AWS S3 inputs

Publicly available files stored on AWS's S3 service can be passed in as inputs, using the file's S3 URI.

Async runs

Set the is_async parameter to true if you would like to run a STAR job asynchronously. See Async Runs for more information.

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.

Databases

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.


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