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Hi.
After I installing TransDecoder, I have run `make test`, but an error has arose like below:
`Can't locate URI/Escape.pm in @INC (@INC contains: /UserHome/user189/transdecoder/TransDecoder/uti…
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Hi we're having some problems with using the TransDecoder.Predict -t transcriptfile.fas function. We started out by doing TransDecoder.LongOrfs -t on all of our fasta files (.fas). We then tried to us…
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Hello!
I am running TransDecoder.Predict and am encountering the following error:
`* Running CMD: /sw/eb/sw/TransDecoder/5.5.0-foss-2020b/util/get_top_longest_fasta_entries.pl transcripts.fa.tra…
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Hello,
I have a bunch of transcriptomes who have been assembled with Trinity all in the same way.
And I have two questions about Transdecoder.
1/Transdecoder seems to have worked well on most…
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Hello,
I get this error:
`Error, cmd: /TransDecoder/TransDecoder-TransDecoder-v5.5.0/util/compute_base_probs.pl /path_to/file.fasta
-O > /path_to_out_dir/base_freqs.dat died with ret 35072 No such…
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Hi,
I'm running now transDecoder for over a week. The command is:
`blastp -query trinity.complete.transDecoder/longest_orfs.pep -db $UNIREF90 -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_thre…
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I use there steps for this process as below
firsly , I ran TransDecoder.LongOrfs
secondly, hmmscan to generate the pfam.domtblout
thirdly, TransDecoder.Predict for better orfs.
I do not know wheth…
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Hi,
It looks like the `cdna_alignment_orf_to_genome_orf.pl` script will swap the strand of an ORF if it is part of a gene with other ORFs predicted by TransDecoder on the opposite strand.
**Exa…
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Good evening,
I am using the last current version of TransDecoder (v5.5.0) to predict the likely coding regions of my transcriptome. I am running TransDecoder.Predict with the '--retain_blastp_hits…
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Hello,
it so happens that Transdecoder gave me several complete proteins that are isoforms. I would like to filter them to keep only one of the isoform. Can this be done by Transdecoder or do I nee…