- STAR genomeGenerate
genomeGenerate option directs STAR to run genome indices generation job.
- STAR alignReads
In this step user supplies the genome files generated in the 1st step, as well as the RNA-seq reads (sequences) in the form of FASTA or FASTQ files. STAR maps the reads to the genome, and writes several output files, such as alignments (SAM/BAM), mapping summary statistics, splice junctions, unmapped reads, signal (wiggle) tracks etc.
- STAR inputAlignmentsFromBAM
Processing of BAM file without re-alignment.
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