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STAR manual 2.7 - Cornell University

star manual 23, 2019 Contents1 Getting Installation.. - in depth and troubleshooting.. Basic workflow..42 Generating genome Basic options.. Advanced options.. chromosomes/scaffolds/patches to include? .. annotations to use? .. in GFF format .. a list of annotated junctions.. small genome.. with a large number of references..73 Running mapping Basic options.. Advanced options.. annotations at the mapping stage.. options .. Using shared memory for the genome indexes..94 Output Log files.. SAM.. attributes.. with Cufflinks/Cuffdiff.. Unsorted and sorted-by-coordinate BAM.. Splice junctions.

--sjdbGTFfile speci es the path to the le with annotated transcripts in the standard GTF format. STAR will extract splice junctions from this le and use them to greatly improve accuracy of the mapping. While this is optional, and STAR can be run without annotations, using annotations is highly recommended whenever they are available.

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