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,
Igor
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,
Igor