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  • Annotated junctions file for STAR

    Hi all,
    Does anyone know where I would be able to get an annotated splice junction file that I could use with STAR? I've been searching for one, but have been having trouble trying to locate one. Also, I believe it should be created from a gff3 file, but am having a bit of trouble figuring out the conversion.

    Thanks for you help

  • #2
    Originally posted by lre1234 View Post
    Hi all,
    Does anyone know where I would be able to get an annotated splice junction file that I could use with STAR? I've been searching for one, but have been having trouble trying to locate one. Also, I believe it should be created from a gff3 file, but am having a bit of trouble figuring out the conversion.

    Thanks for you help
    Hi @lre1234

    you can feed a properly formatted GFF3 file directly to STAR with --sjdbGTFfile /path/to/annot.gff3 --sjdbGTFtagExonParentTranscript Parent , and STAR will extract the junctions from the file.
    Another option is to convert GFF3 to GTF (for instance with Cufflinks utility gffread -T annot.gff3 -o annot.gtf) and then run STAR with simply --sjdbGTFfile /path/to/annot.gtf .

    Cheers
    Alex

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