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Hi,
I have been running Transdecoder (3.0.1 version) for cufflinks results. But it is giving me slightly different results everytime I run it. For example, yesterday it gave me 115923 sequences in t…
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Hi,
I am trying to run transdecoder 5.0.2 but it fail on the last step when i use **TransDecoder.Predict** with the following errors :
```
Running CMD: /usr/local/genome2/TransDecoder-5.0.2/u…
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Hello,
I'd like to use TransDecoder to predict ORF from ISO-Seq.
And my command is like below:
TransDecoder.Predict -t ~/wangrui/transdecoder_treat/Heinz_treat.collapsed.filtered.rep.fa --r…
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Why does such an error occur?
`
-first extracting base frequencies, we'll need them later.
- extracting ORFs from transcripts.
-total transcripts to examine: 121912
[121900/121912] = 99.99% d…
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I don't have much knowledge of Linux, and beginner of transcriptome analysis.
My command is like below.
` [hanqianqian@localhost ~]$ TransDecoder.Predict -t transcripts.fa --retain_pfam_hits pfam.do…
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Hello,
I have a draft genome, and RNA-seq long-reads which I used to generate a reference-based transcriptome with StringTie (GTF), and I also created a reference-free transcriptome (FASTA).
I …
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I don't have much knowledge of Linux, and beginner of transcriptome analysis.
My command is like below.
TransDecoder.Predict -t ../a416agr.corset.m10.fa --retain_blastp_hits blastp/a416agr.blast…
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I am running transdecoder 5.0.2 as a part of my RNA de-novo WDL pipeline.
After I created the folder for my transcripts by:
```
/opt/TransDecoder/TransDecoder.LongOrfs -t ${transcripts}
```
Note:…
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Just a confusion in the wiki page documentation, Step 3: predict the likely coding regions. The information about using the -S flag should be at Step 1: extract the long open reading frames. It is T…
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Hi
When I run my data, a problem occurred as the following:
Running CMD: /export/software/Genome_annotation/transdecoder/TransDecoder-v5.0.2/util/PWM/deplete_feature_noise.pl --features_plus pasa_a…