Align reads to a reference genome using STAR
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
meta2
Groovy Map containing reference information e.g. [ id:‘test’ ]
index
:directory
STAR genome index
star
meta3
gtf
Annotation GTF file
*.{gtf}
star_ignore_sjdbgtf
:boolean
Ignore annotation GTF file
seq_platform
:string
Sequencing platform
seq_center
Sequencing center
log_final
*Log.final.out
STAR final log file
log_out
*Log.out
STAR lot out file
log_progress
*Log.progress.out
STAR log progress file
versions
versions.yml
File containing software versions
bam
*d.out.bam
Output BAM file containing read alignments
*.{bam}
bam_sorted
${prefix}.sortedByCoord.out.bam
Sorted BAM file of read alignments (optional)
*sortedByCoord.out.bam
bam_sorted_aligned
${prefix}.Aligned.sortedByCoord.out.bam
*.Aligned.sortedByCoord.out.bam
bam_transcript
*toTranscriptome.out.bam
Output BAM file of transcriptome alignment (optional)
bam_unsorted
*Aligned.unsort.out.bam
Unsorted BAM file of read alignments (optional)
fastq
*fastq.gz
Unmapped FastQ files (optional)
tab
*.tab
STAR output tab file(s) (optional)
spl_junc_tab
*.SJ.out.tab
STAR output splice junction tab file
read_per_gene_tab
*.ReadsPerGene.out.tab
STAR output read per gene tab file
junction
*.out.junction
STAR chimeric junction output file (optional)
sam
*.out.sam
STAR output SAM file(s) (optional)
wig
*.wig
STAR output wiggle format file(s) (optional)
bedgraph
*.bg
STAR output bedGraph format file(s) (optional)
STAR is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
