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Thank you for this tool.
From my tests I concluded that ORFs are indexed based on a start codon (even without stop codon when reaching the end of a contig)
When an ORF is split in 2 contigs, thi…
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### Describe the bug
If a macro is short enough to fall between two pdn strips then an error should be reported (or the algorithm improved to handle it).
### Expected Behavior
A PDN error rather th…
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With `conda install dammit` version on hpc bridges, only 1 custom aa database:
```
[ljcohen@br018 sbatch_files]$ cat dammit_L_parva-4642625.o
# dammit
## a tool for easy de novo transcriptome anno…
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Hi:
I have correctly installed CNCI on my PC and get an output from CNCI.py, but I don't know how to analysis.
The title is:
Transcript ID index score start end length.
Wha…
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Hi,
While loading the results to Trinotate SQLite database, I am encountering the following error:
Error: column transcript_id is not unique
Error, cmd: echo "pragma journal_mode=memory;
pragm…
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Dear Morgan,
Thank you for developing this fantastic web server and the underlying tools. This is exactly the functionality I was looking for to analyze the genomic context of a limited set of targ…
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Hey,
Is it possible to specify the start codon with OrfM
Thanks,
Ismail
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### Description
Currently, RepairDesign uses a strategy of resizing cells to a target slew in order to perform Post Placement Optimization. With the current methodology, the Resizer ends up "fixing…
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I think there is a problem with the white level for Olympus raws.
It gets set here https://github.com/darktable-org/rawspeed/blob/e5cbf2750893b413e82dbeb7d4cb022018fa4637/src/librawspeed/decoders/O…
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`treesapp abundance` calculates TPM or FPKM for entire query sequences. The depth of coverage, however, is unknown.
A new feature that reports the pile-up along each query sequence's length would b…