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Hi,
I ran TransDecoder on Trinity assembled transcripts and saw the BUSCO value went down post ORF prediction. For example, the BUSCO value was C:94.2%[S:47.2%,D:47.0%],F:1.1%,M:4.7%,n:2326 for th…
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Hello,
I ran GAWN using A. thaliana reference transcripts on a genome assembly from the same species.
I notice quite a few cases in which transcripts seem to map very well to the assembly, but the r…
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I have run Braker2 pipeline on my de novo assembly and RNAseq data.
The output is a gtf file produced by augustus. (sample below)
I would like to use it as input in Transdecoder and then go to Trino…
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Hi Brian,
I hit a problem with running TransDecoder.Predict, as I did have a reasonable number of longest_orfs.cds after running TransDecoder.LongOrfs, something like 226 seqs. However, with runni…
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Hi there,
I met a problem on the result of candidate coding regions, when used TransDecoder to obtain cds regions from a transcript fasta file generated by Trinity. Within the produced *.transdecoder…
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I am working with genes having no BLAST homology, so trying to keep single longest ORF per transcript.
I used
TransDecoder.LongOrfs -S -m 50 etc.
then
TransDecoder.Predict --single_best_only --…
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When I run Transdecoder, on default options, I get few proteins less than 100 amino acids in length. Since the default minimum ORF length for Transdecoder is 100, I am not sure why this is happening.
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Hi, the transdecoder output is based on the transcript coordinate. I have the the gtf file for transcript coordinate in genome. How can I map the CDS gff file from transdecoder to the genome coordinat…
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Hi, there
I used the ORFfinder to find the ORF of the transcripts, and then used the transdecoder to convert the position of the transcripts to the genome. All the data formats meet the requirements…
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I've used TransDecoder as part of the Trinotate annotation suite. I was wondering if there is a way to get a count of the number of candidate coding regions from the TransDecoder output files. Maybe I…