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Hi @arendsee, I'm trying to use the ORF with at least 30nt as unannotated ORF for focal species. I use the gff from ```2d_get_all_orfs.sh``` to instead of search.gff. I got a orphan list use the unann…
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Hi Brian,
I am using TransDecoder on my de novo assembled transcriptome, which has been assembled using illumina short-reads and iso-seq long-reads in rnaSPAdes.
Script: TransDecoder.LongOrfs -…
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Hi there,
Here I'd like to thanks for this excellent tool for assemble short read sequencing data on a protein level, it improved the utilization of reads to a large extent.
When I used the **plass …
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Hi I hope you are well. I am trying to run sprayandpray on a couple of MAGs to decontaminate them.
i have installed the program very well and i have the nr.dmnd file however, i recieve this error wh…
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[uorf html track](https://rpubs.com/Roleren/832825)
Some of the clearly active ORFs in this transcript are not predicted active.
All predicted uORFs by ORFquant are marked with uorf numbers, like uO…
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Not sure if this is a dammit problem, seems like a disk space issue. parallel during lastall seemed unhappy with long records:
```
# dammit
## a tool for easy de novo transcriptome annotation
by…
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Hello, I occasionally run into this issue when running PhySpy:
```
2022-03-28 12:14:53 INFO Welcome to PhiSpy.py version 4.2.21
2022-03-28 12:14:53 INFO Starting PhiSpy.py with the followin…
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Is there a way to incorporate genomes into the pipeline that aren’t from genbank/refseq ?
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It looks like this confusing parameter is often misused. See https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166
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Hi! I was trying to run Padloc on my FAA/GFF file combo from a phage genome (both are outputs from Multiphate2 with ORFs predicted by Phanotate). Padloc failed with the error message
`ERROR >> 3 pr…