Michael Alonge
Michael Alonge
Thanks and happy new year! Let's keep this open until I fix this bug.
Hi Dario, I think the first thing to try is to use Nucmer. I suggest following the instructions in #48. If you think you need more specificity to distinguish between...
Hi there, Good to see that purging haplotigs helped out. It's hard to say how these smaller contigs may have affected things without digging into things a bit. Usually, alignment...
Hi there, Could you share your command along with the content of `ragtag.scaffolds.stats`. Perhaps you could also provide more details about the reference and query assemblies, i.e what species and...
Hi there, So the vast majority of sequence is being assigned to contigs. One observation is that even though you are using `ragtag.py correct`, you are not actually using the...
Hi there, First, to help us debug, you may consider rerunning using the `--debug` command. For each of the individual scaffolds, do the AGP files indicate any scaffolding? Or do...
Thanks so much for the details. I can't see any obvious problems, so would you be willing to share the data so that I could take a look myself? If...
Hi there, Your command seems to be off because there should be a fasta file instead of a txt file. Please read the [Wiki](https://github.com/malonge/RagTag/wiki/merge) and let me know if you...
Hi there, So I will first comment on the original error: `ValueError: Input AGPs do not have the same set of components` In order to use `merge`, the AGPs file...
sure you can email me at `[email protected]`. I can take a look at the AGP files and see what is going on.