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Hi,
Since UTR is a part of the exon feature in molecular biology, I attempted to extend the start coordinate of the first exon (for forward strand transcripts, 5’ -> 3’) or the end coordinate of the…
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Thankyou for building the new tool to complement Orthofinder.
The features are currently required in NCBI feature format. Is it possible to implement a feature to use a local GFF file instead as an i…
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I am a PhD student doing a collaborative project between Trinity College Dublin and UCLondon and am using MCScanX. I am just getting to know the tool and have been trying to use the test data availabl…
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I have already run Pyrodigal on ~50k genomes and would like to run GECCO on these genomes without rerunning Pyrodigal in the backend. Is there similar usage to `antiSMASH` where precompute gene model…
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Hello,
I have trouble in using prophET. I validated my GFF file and i still receive this error "The following line does not have 9 columns separated by , a GFF format requirement.
Check if the col…
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Hi,
I want to annotate a Verticillium Genome via command line. I installed augustus and all neccesary stuff to get it work and tested with the example data -> worked.
My Verticillium Genome is als…
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Hello developers!
Thank you for such an great tool!
I wonder if there is an option or way to keep the pyrodigal cds predictions in a gff format or convert the tsv coordinates to gff
Thank you…
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Not sure if it is a software problem or if my gff format does not meet the requirements of the software. It is recommended that authors provide an example-gff file that can be run.
```
Scanning Sequ…
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Good afternoon,
I've been trying desperately to annotate my final vcf file as the last step for smoove, using genome version hg38.
However, when I use the gencode gff3 file, I get the following er…
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Hi,
could someone explain me why the feature type for a line in a GFF is not taken from the third GFF filed but `bcftools csq` expect each gene and transcript with a prefix (e.g., `gene:` or `trans…
fbemm updated
3 years ago