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alexdobin / STAR

RNA-seq aligner
MIT License
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Genome indexing #2166

Open cottonrnr opened 3 months ago

cottonrnr commented 3 months ago

Hello Alex,

The annotation of my reference genome is in gff3 format. For genome indexing, I used: STAR --runMode genomeGenerate --runThreadN 40 --genomeDir genome \ --genomeFastaFiles ref.fasta --sjdbGTFfile ref.gff3 --sjdbGTFtagExonParentTranscript Parent \ --sjdbOverhang 100

but the geneInfo.tab showed: MissingGeneID MissingGeneID MissingGeneType

then ReadsPerGene.out.tab got no counts: N_unmapped 3180903 3180903 3180903 N_multimapping 0 0 0 N_noFeature 3396349 3723454 20509453 N_ambiguous 0 0 0 MissingGeneID 17496180 17169075 383076

How can I fix the genome indexing issue?

Thanks!

Chunda

Svnipni commented 3 months ago

Having the same issue. Tried with cufflinks' readgff but ending up with the same issue. running STAR --runThreadN 16 \ --runMode genomeGenerate \ --genomeSAindexNbases 10 \ --genomeDir 101_index \ --genomeFastaFiles 101_v3.01.fna \ --sjdbGTFfile 101_v3.01.gff

head 101_v3.01.gff:

`##gff-version 3

sequence-region gnl|Bactopia|101_v3.01.01_1 1 724572

sequence-region gnl|Bactopia|101_v3.01.01_2 1 579375

sequence-region gnl|Bactopia|101_v3.01.01_3 1 479507`