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I just had a look at DIAMOND again. They added some time ago the capability of obtaining XML output instead of only tabular. I have to say I am **hugely** impressed ... it was able to perform the alig…
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Issues we need to solve:
- Sometimes transcripts are classified as open even when there is a methionine clearly downstream of the imputed start. We have to move the thick_start downstream in those cas…
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At the moment Daijin executes TransDecoder without asking for the minimum length of the ORF to be found. The default, 100 AA or 300 bps, _is too high for Mikado_ as the tool relies on the coding signa…
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A few questions re PP.
1) What is a decoy database?
In the command below
I get
`WARNING: No decoys with label DECOY_ were found in this dataset. reverting to fully unsupervised method.`
2) Sh…
sr320 updated
7 years ago
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```
[~/mnt/dammit]$ dammit databases --install --database-dir ~/mnt/dammit --full --busco-group metazoa
========================================
dammit! a tool for easy de novo transcriptome annota…
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Hello,
I am trying to run dammit and I keep getting the error messages below, which I have tried to fix with no success. Any suggestions will be helpful! -Molly
```
--- Database results
A…
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Hi I'm trying to use PFAM `--retain_pfam_hits` option with TransDecoder.Predict
I'm getting no error or results at all regarding PFAM.
I've downloaded both `Pfam-A.hmm.gz` and `Pfam-B.hmm.gz` and joi…
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The pipeline works perfectly with Trinity/PASA evidences, but.... tbastn/Exonerate. Having just 1 exonerate alignment, does it mean that UniProtKB evidences will not be used in gene prediction? Any id…
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```
$ TransDecoder.Predict
No transcript file (-t)
NAME
Transdecoder - Transcriptome
Protein Prediction
USAGE
Required:
-t transcripts.fasta
Comm…
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It seems for crappy contigs this is reported several times per each. I do not understand the english in there but probably there is no ORF found in the particular contig. UPDATE: the contigs had same …