usage: star_align.py [options]
ICGC RNA-Seq alignment wrapper for STAR alignments.
Required input parameters:
--genomeDir GENOMEDIR
Directory containing the reference genome index
(default: None)
--tarFileIn TARFILEIN
Input file containing the sequence information
(default: None)
optional input parameters:
--out OUT Name of the output BAM file (default: out.bam)
--workDir WORKDIR Work directory (default: ./)
--metaDataTab METADATATAB
File containing metadata for the alignment header
(default: None)
--analysisID ANALYSISID
Analysis ID to be considered in the metadata file
(default: None)
--keepJunctions keeps the junction file as {--out}.junctions (default:
False)
--useTMP USETMP environment variable that is used as prefix for
temprary data (default: None)
--weakRGcheck only perform weak RG record check and generate generic
RG ID in case of a single alignment file with multiple
RG records present. Use with caution! (default: False)
-h, --help show this help message and exit (default: False)
STAR input parameters:
--runThreadN RUNTHREADN
Number of threads (default: 4)
--outFilterMultimapScoreRange OUTFILTERMULTIMAPSCORERANGE
outFilterMultimapScoreRange (default: 1)
--outFilterMultimapNmax OUTFILTERMULTIMAPNMAX
outFilterMultimapNmax (default: 20)
--outFilterMismatchNmax OUTFILTERMISMATCHNMAX
outFilterMismatchNmax (default: 10)
--alignIntronMax ALIGNINTRONMAX
alignIntronMax (default: 500000)
--alignMatesGapMax ALIGNMATESGAPMAX
alignMatesGapMax (default: 1000000)
--sjdbScore SJDBSCORE
sjdbScore (default: 2)
--alignSJDBoverhangMin ALIGNSJDBOVERHANGMIN
alignSJDBoverhangMin (default: 1)
--genomeLoad GENOMELOAD
genomeLoad (default: NoSharedMemory)
--genomeFastaFiles GENOMEFASTAFILES
genome sequence in fasta format to rebuild index
(default: None)
--outFilterMatchNminOverLread OUTFILTERMATCHNMINOVERLREAD
outFilterMatchNminOverLread (default: 0.33)
--outFilterScoreMinOverLread OUTFILTERSCOREMINOVERLREAD
outFilterScoreMinOverLread (default: 0.33)
--twopass1readsN TWOPASS1READSN
twopass1readsN (-1 means all reads are used for
remapping) (default: -1)
--sjdbOverhang SJDBOVERHANG
sjdbOverhang (only necessary for two-pass mode)
(default: 100)
--outSAMstrandField OUTSAMSTRANDFIELD
outSAMstrandField (default: intronMotif)
--outSAMattributes OUTSAMATTRIBUTES
outSAMattributes (default: ['NH', 'HI', 'NM', 'MD',
'AS', 'XS'])
--outSAMunmapped OUTSAMUNMAPPED
outSAMunmapped (default: Within)
--outSAMtype OUTSAMTYPE
outSAMtype (default: ['BAM', 'SortedByCoordinate'])
--outSAMheaderHD OUTSAMHEADERHD
outSAMheaderHD (default: ['@HD', 'VN:1.4'])
--outSAMattrRGline OUTSAMATTRRGLINE
RG attribute line submitted to outSAMattrRGline
(default: None)
--outSAMattrRGfile OUTSAMATTRRGFILE
File containing the RG attribute line submitted to
outSAMattrRGline (default: None)
--outSAMattrRGxml OUTSAMATTRRGXML
XML-File in TCGA format to compile RG attribute line
(default: None)