How to add --sjdbGTFfeatureExon to star

Hey everyone,

currently I am struggling with aligning my seq data to my reference sequence. The annotation file hasn’t any exons, just CDS, gene and region and therefore I can’t use STAR aligner. Are there any possibilities to add --sjdbGTFfeatureExon to change the feature of the annotation file??


Hi @benediktp
maybe consider mapping reads without gene annotation and count reads mapped to genes using featureCounts or htseq-count. Do you work with bacterial data? In this case you probably don’t need gapped aligner.
Kind regards,

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