BRAKER miss some genes despite of RNA-Seq evidence

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4.8 years ago

Ric ▴ 430

Hi, I ran braker.pl --UTR=on --genome=$1 --bam=$2 --species=$3 --cores 20 --softmasking --gff3 but in few cases, BRAKER did not predict any genes where there is RNA-Seq alignment.

Is there a way to get still gene predictions for those missing areas?

Thank you in advance,

RNA-Seq genome Assembly BRAKER • 1.1k views

ADD COMMENT • link updated 4.8 years ago by ATpoint 81k • written 4.8 years ago by Ric ▴ 430

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Rna-seq are not necessarily from protein coding genes. Have you seen any ORF that make you think that a gene is missing? Otherwise you should check. If there is no ORF Augustus will not be able to predict anything.

ADD REPLY • link 4.8 years ago by Juke34 8.5k

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apart from what Juke-34 already mentioned, you have to keep in mind that all these tools (approaches) have the goal to correctly predict as much genes as possible. This of course does not mean that all genes will be correctly predicted (if at all) but that the majority of the genes should be correct (or as good as). A consequence of this can be that some genes will be perhaps missed if by that eg. a 100 others might be correct

ADD REPLY • link 4.8 years ago by lieven.sterck 15k

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