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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?

  • $\begingroup$ Cross-posted, biostars.org/p/477807, please don't do that, and please get used to properly format your question with the code option, right now it looks messy. $\endgroup$ – ATpoint Dec 8 '20 at 10:11
  • $\begingroup$ Did you try indexing your bam file? $\endgroup$ – user438383 Dec 8 '20 at 13:02

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