Description

Align reads to a reference genome using STAR

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

index (directory)

STAR genome index

star

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

gtf (file)

Annotation GTF file

*.{gtf}

star_ignore_sjdbgtf (boolean)

Ignore annotation GTF file

seq_platform (string)

Sequencing platform

seq_center (string)

Sequencing center

Output

Name (Type)
Description
Pattern

bam (file)

Output BAM file containing read alignments

*.{bam}

log_final (file)

STAR final log file

*Log.final.out

log_out (file)

STAR lot out file

*Log.out

log_progress (file)

STAR log progress file

*Log.progress.out

versions (file)

File containing software versions

versions.yml

bam_sorted (file)

Sorted BAM file of read alignments (optional)

*sortedByCoord.out.bam

bam_transcript (file)

Output BAM file of transcriptome alignment (optional)

*toTranscriptome.out.bam

bam_unsorted (file)

Unsorted BAM file of read alignments (optional)

*Aligned.unsort.out.bam

fastq (file)

Unmapped FastQ files (optional)

*fastq.gz

tab (file)

STAR output tab file(s) (optional)

*.tab

junction (file)

STAR chimeric junction output file (optional)

*.out.junction

wig (file)

STAR output wiggle format file(s) (optional)

*.wig

bedgraph (file)

STAR output bedGraph format file(s) (optional)

*.bg
included in
circrna marsseq rnadnavar rnafusion rnaseq rnasplice rnavar viralintegration
authors
Github user kevinmenden Github user drpatelh Github user praveenraj2018
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

star
MIT

STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

github.com/alexdobin/STAR 10.1093/bioinformatics/bts635