Zoe Clarke

Incorrect parent features from convert_tRNAScanSE_to_gff3.pl

2

Hi there, First off, thank you so much for making this script! I'm trying to incorporate filtered tRNAScanSE results into my genome annotation. However, the results from this script are...

Error when blat begins

5

Hello! I am experiencing an error with Flo that I was hoping you might be able to help me with. Rake aborts when blat begins, I believe. I searched for...

When the dots shrink down in size from increasing the # of genes per cluster to show, the gene names don't shrink down so there is more than one dot...

Missing genes not in unmapped_features.txt

2

Hi there, I really enjoy your tool! It's been very helpful for me, as I've been annotating the genome of a less common model organism. I am annotating a new...

$genome not recognized in reference tdv file

4

Hello! I am hoping to use OrthoFiller and am having an issue with my reference species data. When I run OrthoFiller, I get the following error: `Gtf file /path/species_files/genomic.gtf contains...

Results from DropletQC not matching Velocyto

2

Hi there, First off, thank you so much for the creation of this tool! It's extremely helpful and I use it all the time. I've been looking further into gene-specific...

LiftOff generates better BUSCO scores than LiftOn

2

Hi there, I was testing LiftOff and LiftOn to see which one is "best" for genome annotation. I was looking at some RefSeq genomes, lifting the brown-headed cowbird and red-winged...

Hi there! I'm trying to install LiftOn with pip. I see LiftOn requires networkx>=2.4, but running `pip install LiftOn` seems to be looking for a more recent version of networkx...

Hi there, Love your tool! I was wondering if you had any recommendations for how related species need to be when lifting from one genome to another. Perhaps the same...