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hey,
I first ran TransDecoder.LongOrfs and then Predict and I got that error message:
Selecting best orfsError, cannot find file blastp.outfmt6 at /usr/local/packages/transdecoder-5.7.1/util/se…
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It is my understanding that OrfM outputs continuous stretches of codons without a stop codon in the middle, but I am getting output with embedded stop codons, or what I believe are stop codons. I trie…
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Sorry another issue. I have loaded the project into R using loadSQM, but when trying to subset taxa I am getting an error which seems to be driven by an issue with the orf$table
```
water$orfs$tab…
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* ribotricer version: 1.3.3
* Operating System: Linux
### Description
Just experimenting with `--stranded`
### What I Did
```
ribotricer detect-orfs \
--bam SRX11780888_chr20.bam \
…
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The upstream ORFS `save_images.tcl` file has been changed again and this is causing the flow to fail with the latest version of OpenROAD. (related to #256).
The LDO flow in #288 failed due to the sam…
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Hi, I am running CAT to annotate contigs from metagenomes that are known to be E. coli by several other approaches. For example, greater than 99% average nucleotide identity with reference E. coli ge…
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Hi DeepRibo developers,
thanks for making this package, it is very convenient to work with.
I'm currently testing the predictions from DeepRibo for a bacterium where we have new RiboSeq data.
I a…
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## Negative controls:
- We want negative controls to:
- Have no signature confirmed by existing datasets.
- Having no signature usually is equivalent to having low replicate correlation…
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## Expected Behavior
I'm trying to run `clusterupdate`, but I'm running into the error:
```
diffseqdbs /ebio/abt3_projects/software/dev/Struo2/tests/output_n10/genes/cluster/genes_db /ebio/abt3…
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Hi!
I would like to run the module A for an eukaryote organism (Mus musculus). For now the analysis has been running for a month (and I think it will take a lot more time).
I've been looking at bo…