Eduardo Gonzalez Grandio

queryTxObject adds "chr" to seqlevels, creating a mismatch with BSgenome seqlevels

10

I am using `crisprDesign `with a custom genome (Nicotiana tabacum K326) that has 24 chromosones and several scaffolds: ``` library(BSgenome.NtabacumK326.sierro2024) K326_bsgenome seqlevels(K326_bsgenome) [1] "Un00001" "Un00002" "Un00003" "Un00004" "Un00006" "Un00007" "Un00008"...

geom_beeswarm() misaligned with geom_boxplot(position_dodge2(preserve = "single")) when groups have unequal numbers of subgroups

1

Hello, When overlaying geom_beeswarm() on top of a dodged geom_boxplot() with preserve = "single", the beeswarm points do not always align with their corresponding boxplots if some x-axis groups have...

Hello, I am trying to use the conda version of `funannotate `with a fungal genome. I have run all the tests successfully, but when I am using `funannotate train` on...

Hello, I have run into the following error: ``` ERROR in file /opt/BRAKER/scripts/braker.pl at line 7866 Failed to execute cat /mnt/d/seq_data/braker3/ppax/augustus_tmp/371.001.KB644898.1.fa.1..423438.gff >> /mnt/d/seq_data/braker3/ppax/augustus.tmp1.gff ``` When I look into the .log...

ERROR in file /opt/BRAKER/scripts/braker.pl at line 6893 Failed to execute: /usr/bin/perl /opt/Augustus/scripts/optimize_augustus.pl

3

Hello, I am using the singularity `braker.pl version 3.0.8` with RNAseq and protein data. ``` singularity exec \ --mount type=bind,src=/mnt/d/Ppax_genome_v1.0,dst=/mnt/d/Ppax_genome_v1.0 \ --mount type=bind,src=/mnt/d/hisat2_mapped,dst=/mnt/d/hisat2_mapped \ braker3.sif braker.pl \ --genome=/mnt/d/Ppax_genome_v1.0/GCA_000347475.1_Ppaxilli_v.1.0_genomic_trimmed.fna \ --prot_seq=Fungi_trimmed.fa...