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I am trying to run htseq-count for carrying out rna-seq analysis for solanum tuberosum and i used the following command:
htseq-count --format bam --order pos -s no -a 10 -t exon -i gene_name --idattr gene_id SO_8612_L1.bam GCF_000226075.1_SolTub_3.0_genomic.gff > L1_htseq_count.tsv and im getting an error message saying: [E::idx_find_and_load] Could not retrieve index file for 'SO_8612_L1.bam' Error processing GFF file (line 12 of file GCF_000226075.1_SolTub_3.0_genomic.gff): Feature exon-XM_015312074.1-1 does not contain a 'gene_id' attribute [Exception type: ValueError, raised in features.py:326]
How to resolve this? and also can gff be used instead of gtf file. what is the standard gtf file used for Solanum tuberosum?