Alex,
I'm trying to create a genome index for Xenopus tropical using a gff3 file and I'm having trouble trying to figure out what I should specify for --sjdbGTFtagExonParentGene. When I run the program, no program breaking errors occur, however, the Log.out file contains the warning;
WARNING: while processing sjdbGTFfile=/usr/lusers/achits/achits/genomes/Xtropicalisv9.0.Named.primaryTrs.gff3: no gene_id for line:
here is my code:
STAR --runThreadN 16 \
--runMode genomeGenerate \
--genomeDir ~/achits/genomes/STARTest/ \
--genomeFastaFiles /home/achits/achits/genomes/Xtropicalis9/Xtropicalis.v9.repeatMasked.fa \
--sjdbGTFfile /usr/lusers/achits/achits/genomes/Xtropicalisv9.0.Named.primaryTrs.gff3 \
--sjdbGTFtagExonParentTranscript Parent \
--sjdbOverhang 100 \
--sjdbGTFfeatureExon CDS
I believe this can be solved with the --sjdbGTFtagExonParentGene flag but I'm having trouble knowing what to specify for this? I have attached a copy of my Log.out file and a 'head' of my gff3 file. My thought right now is that "ID" should be specified to be used for it but I'm not quite sure.
Thank you,
Alex
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Alex
Wills Lab | University of Washington