Annotated junctions file for STAR

[lre1234]

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

[alexdobin]

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