kushalsuryamohan

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Busco scores of predicted proteins much lower than busco of genome

Hi @jguhlin and @nextgenusfs, I have a similar issue where using RNA-seq data as training for PASA seems to give very poor gene models (BUSCO completeness of ~20%) despite the...

Busco scores of predicted proteins much lower than busco of genome

Hi @jguhlin, thanks for getting back to me. Is this the directory you refer to that contains the augustus.gff3? > -bash-4.2$ ls -lrt busco_only_training/predict_misc/ > total 2740908 > -rw-rw-r-- 1...

Lower than expected BUSCO score for funannotate predict-derived gene models compared to genome and transcriptome BUSCO scores

Hi Jon @nextgenusfs, Sure I'd be happy to share this (although it is unpublished data so I'd appreciate it being kept private). How do you propose I share the data?...

Lower than expected BUSCO score for funannotate predict-derived gene models compared to genome and transcriptome BUSCO scores

Will do. Can you share your email address, please?

Lower than expected BUSCO score for funannotate predict-derived gene models compared to genome and transcriptome BUSCO scores

Hi @hyphaltip and @nextgenusfs , out of curiosity and to dig deeper into this, I extracted transcripts from the augustus gff3 (from the predict_misc directory) and ran BUSCO. Here are...

Lower than expected BUSCO score for funannotate predict-derived gene models compared to genome and transcriptome BUSCO scores

Hi @nextgenusfs, I've uploaded the genome and PASA GFF3 and sent you an email with access details. Can you also see my previous post above? It might help you troubleshoot...