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How Splice Junction database(SJ.out.tab) is generated from GTF(ENSEMBL) and Reference Genome (GRCh38) using STAR Aligner during Genome indexing

As am not an expert in the field, Hence I could like to know few basic concept on how STAR generate Splice Junctions Database(sjdb/SJ.out.tab) while indexing the reference genome with gtf file.

I find information from STAR Manual: http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf

Under session : 8.5 Splice Junctions Database

But couldn't able to understand how only with reference genome and GTF file, Splice junction file is constructed within the genome directory.

I really appreciate your valuable response in advance.

star hisat gtf splice junction assembly
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updated by yywang113 • yywang113 • written by inambioinfo • inambioinfo

1 answer

This paper may help you understand more about the RNA mapping steps used in STAR.

Hope it helps, Thanks.

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updated by Ram Ram • written by yywang113 • yywang113

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