calizilla

Thank you @lalalagartija that docker container is the saviour! I have a conda installation of funannotate that seg faults at CodingQuarry, a manually installed CodingQuarry that also seg faults, but...

Hi @dingcaojin - I don't use docker as it's not permitted on the cluster I work on. I used the below command to pull the docker file as a singularity...

@dingcaojin I'm happy to have helped :-) Note that if you run CodingQuarry manually, outside of funannotate instead of modifying `library.py` to run it with sungularity, to make the adjustments...

Hi Jennifer, I am experiencing this also. I created a custom db and have the same error as charlottecc. I followed the custom database creation steps carefully and there were...

Hi Dario I have checked your data and can see that alt-aware mapping was carried out. You have the .alt index file in place, the alt contigs have the AH...

It does appear odd that the mapping quality of the primary alignment has not been assigned > 0. I am also interested to note that both alt locations are listed...

Let's wait to hear what Heng Li has to say regarding https://github.com/lh3/bwa/issues/342 before assuming the bwa-kit is buggy. There may be a sound reason as to why the MAPQ of...

Thanks for the suggestion Dario. The simplest solution would be to clone a new repo and re-align using the different reference genome. As the mapping qualities and tags will be...

Hi Dario. Heng Li has recomemnded against this genome ONLY IF the user is not using ALT-aware tools. this repository contains a workflow that uses an alt-aware tool (bwa-kit) so...

Hello, I would be happy to help you run the workflow if you could please provide some more information on what you are having difficulties with? As far as I...