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Hello,
is there any way to chose where the output files for TransDecoder are created?
Best,
Lea
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- [x] Identify user parameters for clustering that we might want to make user-specifiable. (e.g. secondary clustering with cd-hit)
- [x] Add kmer selection for different assemblers (e.g. Trinity, Tra…
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Hello,
Is it possible to run Transdecoder on files that have "N"'s for bases without producing an error?
Thanks
Madison
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Hi,
Scallop with TransDecoder has done a really good job. I used the Scallop results with TransDecoder. Next, I would like to reduce the number of isoforms per gene. I noticed that not always the fir…
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Hi!
I have assembled my transcripts with Trinity using stranded RNA-seq data and after I predicted ORF with Transdecoder. After TransDecoder.Predict I noticed that for some transcripts I have more th…
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Is is possible for TransDecoder to output:
1)only complete ORFs (those with start and stop codons)
2)the current output plus any transcripts without ORFs
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I have been trying to run TransDecoder to identify ORFs in a set of transcripts. However, multiple transcripts keep outputting partial ORFs as their first result (i.e. labeled ".p1"). I have looked at…
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Running TransDecoder.LongOrfs with a sequence (that should only by 99AA long when translated) returns a 99AA sequence even when the minimum protein length is set to 100.
This appears to be an off-by…
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First off, I want to whole heartedly thank you for creating this package. I've been dealing with this obscure Eukaryote with no published genome... I have a bunch of RNA-seq and the collaborators wan…
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Hi,
Would it be possible to add an option for TransDecoder not to consider the sequence context around the start codon for cases where an earlier start codon isn't found in the transcript? In my ex…