Zeynep Akdeniz issues

Results 5 issues of


                                            Zeynep Akdeniz

glimmergff_to_proteins.py / Reordering Fasta file

Hi, Thank you for this very useful script!! I was wondering if it's possible to create the protein multi fasta file with the order of ref_file (contigs) instead of the...

glimmergff_to_proteins.py / Alternative Codon Table

Hi, I'd like to add this issue for those who'd like to use the script with an alternative codon table. Example: If you want to translate the sequence with a...

etraining / alternative codon table / in_frame_stop_codon

Hi, I'm working on training Augustus for a new species by using the alternative codon table 6. I've changed the stop codon probabilities from species.paramaters.cfg file. However, I'm still getting...

reads that thrown out from the assembly

Hi, Is there a way to reach reads that have been thrown out during the assembly process? I've run Masurca with Flye and I was wondering if the output directory...

CAFE5 run is taking forever

I've been running CAFE5 with around 12,000 Orthogroups on 4 species by using 32 CPUs. It's been a week and it is still searching for lambda parameters. I haven't played...