Lauren Coombe

Thanks for looking at this @SaberHQ! Please correct me if I'm wrong, @SimonHegele - I believe the issue is that the IDs _did_ match between the quantification file and the...

Hi @desmodus1984, 1. In our paper (https://doi.org/10.1093/bioinformatics/btaa253), we compared ntJoin to Ragoo, which was was the predecessor of RagTag. I haven't done any tests with the newest RagTag version. 2....

Hi @desmodus1984, Ok, thanks for clarifying! There are a couple of considerations that you could make here: 1. I'd suggest using the scaffolded draft from the same species in a...

Hi @desmodus1984, For the zero-depth regions, unfortunately you couldn't use ntJoin directly because it doesn't use any read information in the execution. You would expect full contigs with zero coverage...

Hi @yaoxkkkkk, The amount of memory required will really depend on the dataset that you are training on. On my end, training using `--fastq` with the HG002 ONT dataset used...

Hi @pdimens, Yes, you are right - `arcs-make` decides on the prefix of the files based on the input scaffolds and parameters. Are you thinking that you would like all...

Yes, for sure. Thanks for that suggestion (I know that the current prefix names can be quite long...) - I'll take a look at making that adjustment in the next...

Hi @pdimens, So I spent some time looking at `arcs-make` to see what tweaks that could be made. Unfortunately, adding that prefix parameter would not be as straightforward as I...

Thanks @pdimens! I think we're thinking along the same lines with your second suggestion and my soft-link suggestion. If we just have a soft-link to the file with your the...

Always happy to get suggestions from our users! I'll try to make those changes in the next week or so - will keep you updated.