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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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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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- [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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[As per this site](https://cryptogenomicon.org/2011/05/27/hmmscan-vs-hmmsearch-speed-the-numerology/), `hmmsearch` is significantly faster and parallelizes better than `hmmscan` (at least when searchi…
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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 a question about the script that does the translation of ORFs to genome coordinates. There are a fair number of sequences that have the error 'shouldn't have a minus-strand ORF on a spli…
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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 would like to know the frame of the predicted ORF, can you please guide me how to get this information I don't see in any of transcripts.fasta.transdecoder.* files ?