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Hi @adeslatt,
I attempted to run the baby nextflow code to run Transdecoder.
I correct a few minor bugs (e.g., lr_orfcalling.nr -> lr_orfcalling.nf).
The help message displayed correctly.
The ne…
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Hi,
I was wondering if there was a simple way to add features to the talon GTF such as CDS. Any recommendations?
TIA
Renee
rsalz updated
3 years ago
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Hello,
I am getting an unusual error in the mikado serialize step of the pipeline. The following is the serialise.log file. Obviously, I prepared the orf bed file from mikado_prepared.fasta using t…
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Hi,
I am getting error code 106 during the TransDecoder parsing stage in EnTAP v0.10.7-beta.
```
Error in TransDecoder parsing of file at: /home/zoo/zool2474/guy/eli/transcriptomics/DAS/DAS_trin…
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Hi,
I was able to run Evolinc with the test data but now I am getting an error when using it on braker genome annotations. This is the error message
```
Tue Mar 9 17:39:39 UTC 2021
No fasta index…
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Command:
```
TransDecoder.LongOrfs -t rnaspades_output/843/transcripts.fasta --output_dir ./transdecoder_output/843 --gene_trans_map ./rnaspades_output/843/gene_trans_map.tsv
```
Fasta file:
…
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Hi all,
I'm running into a problem using Mikado serialise, wherein the blast serializer is crashing.
I'm running Mikado v2.0.2
I created an input file (`Amoebidium_mikadoInput_list`), which refer…
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Hi all,
I ran `microsynteny.py -b no_remark.out -q Q.no_remark.mRNA.gff3 -d NbR.no_remark.mRNA.gff3 -D "|" --make-gff > Q-NbR.no_remark.mRNA.microsynteny.gff3`
Diamond's BLASTp output:
```
NBqld…
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Hi IUC - I'd like to request an update to the Transdecoder tool.
Current tool shed version is 3.0.1 (from Oct 31, 2016)
Latest version is 5.5.0 (from Oct 26, 2018)
There's been a few relevant c…
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Hi Brian et al.,
Many years ago I set up Trinotate_r20131110 and noticed that I never got a signalp.out file from any of the transcriptomes that we annotated. I assumed that this was due to the non…