--sjdbGTFtagExonParentGene

[Alex Chitsazan]

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

--

Alex

Wills Lab | University of Washington

[Alexander Dobin]

Hi Alex,

most gff3 files do not include the parent gene for each exon, only parent transcript.

You only need it if you are planning to use --quantMode GeneCounts

In this case it's best to transform the GFF3 into GTF, for instance with gffread from Cufflinks package:

gffread -T In.gff3 -o Out.gtf

Cheers

Alex

[Alex Chitsazan]

Ah gotcha, thanks!

Alex