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carolzhou / multiPhATE2

multiPhATE with comparative genomics
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missing annotations in final gff for tRNAs #19

Closed xvazquezc closed 3 years ago

xvazquezc commented 3 years ago

Hi there,

the current output in the phate_sequenceAnnotation_main.gff does not include a proper annotation for the tRNAs found, i.e. it doesn't specify the tRNA type. tRNAscan-SE provides both the ligand and the anticodon in its output so it would be great if that some of this info were integrated in the final annotation.

Current:

chr1    PhATE   trna    132848  132924  80.8    -       .       ID=chr1_trna_1;
chr1    PhATE   trna    132676  132758  57.3    -       .       ID=chr1_trna_2;
chr1    PhATE   trna    132608  132674  21.5    -       .       ID=chr1_trna_3;annot1=pseudo
chr1    PhATE   trna    132273  132348  87.5    -       .       ID=chr1_trna_4;

Possible annotation:

chr1    PhATE   trna    132848  132924  80.8    -       .       ID=chr1_trna_1;annot1=tRNA-Pro
chr1    PhATE   trna    132676  132758  57.3    -       .       ID=chr1_trna_2;annot1=tRNA-Leu
chr1    PhATE   trna    132608  132674  21.5    -       .       ID=chr1_trna_3;annot1=tRNA-pseudo
chr1    PhATE   trna    132273  132348  87.5    -       .       ID=chr1_trna_4;annot1=tRNA-Thr

Alternative (includes anticodons)

chr1    PhATE   trna    132848  132924  80.8    -       .       ID=chr1_trna_1;annot1=tRNA-Pro(TGG)
chr1    PhATE   trna    132676  132758  57.3    -       .       ID=chr1_trna_2;annot1=tRNA-Leu(TAG)
chr1    PhATE   trna    132608  132674  21.5    -       .       ID=chr1_trna_3;annot1=tRNA-pseudo
chr1    PhATE   trna    132273  132348  87.5    -       .       ID=chr1_trna_4;annot1=tRNA-Thr(TGT)
carolzhou commented 3 years ago

I see what you mean. Yes, that would be useful to include. I will work on it.

carolzhou commented 3 years ago

tRNA reporting has been improved. Listed is the codon/anticodon for each prediction.