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12-15-2015, 08:24 AM
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#1 |
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Senior Member
Location: US Join Date: Aug 2011
Posts: 106
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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 |
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12-16-2015, 01:31 PM
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#2 | |
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Senior Member
Location: NY Join Date: Feb 2009
Posts: 161
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Quote:
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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| Tags |
| junctions, splice junction, star aligner |
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