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Hello, I have run gff3_QC and gff3_fix on my two gff files but I am getting the following error while using the gff3_merge command
```
gff3_merge -g1 Qalba_4.3.1.HapA.genes_corrected.gff3 -g2 QalbaA…
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Current implementation only supports BED window specification, so add support for specifying windows via GFF annotations. Also consider: GTF support, other file formats.
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Hi whoever sees this post,
I am running BRAKER with only proteins as the input for this stage. I continuously got this message - ERROR in file /opt/BRAKER/scripts/braker.pl at line 4178. I tried to…
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Hello,
I want to run core gene analysis with Spine locally and also want to include gff file, I use -f for genome_files.txt which containing paths to fasta file and their coresponding gff files. It i…
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Hi, all
1. I use these 5 speices to identify HCEs, and use [gold fish method](https://www.science.org/doi/10.1126/sciadv.aav0547) to get muti-align file(Xenopus_tropicalis_mulitway.maf) .
![imag…
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## Expected Behavior
No error.
## Current Behavior
```
Not enough GFF files are provided. Some results might be omitted
tmpFolder/15806226240676100088/createsetdb.sh: line 130: 9468 Segmentati…
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I encountered an error, "error, no valid sequences were found," while using BRAKER for gene prediction, causing the process to stop. Based on responses to similar issues, there seem to be two main cau…
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Hi,
Is there a pipeline to obtain required input annotation files for any other genomes? For example, I have rice genome sequences in fasta and annotations in gff format, how to prepare the requir…
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Hi Ian,
Thanks for making this great tool available!
I've been able to get this running in a Singularity container on my machine, but I would like to have output in GenBank format (I can't find an…
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Hi,
I am using the newest version 0.0.2 isONclust3 and would like to try the `--gff` flag and see what is the different between the default and with the `--gff` flag
here is my command
```
a…