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Collapsing of isoforms, transcript annotation, and transcriptome quality assessment (script: collapse_annotate_clean_transcriptomes.sh, busco.sh) Highly similar isoforms generated from the Trinity assembly were further collapsed to keep only the longest isoform as a representative using CD-HIT 48 (parameters: -c 0.99 -G 0 -aL 0.3 -aS 0.3) as differential abundance estimation has been shown to be more accurate at the gene versus isoform level 49
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