Dong-Ha Oh

Thanks, Ilia, for the quick response :) I have a few more questions regarding the "non-overlapping" part since this appears a requirement for maf2synteny. 1. The 1st alignment from the...

Thanks a lot, Ilia. I noticed that sometimes the first sequence of the SibeliaZ output maf was on - strand direction and some tools (e.g. phyloFit of PHAST) don’t like...

> Could you also show how to calculate the information content for custom GOA in id2go format (i.e., gene ID in the 1st column and GO terms concatenated with ";"...

Sorry for the hitchhiking... I have the exact same error message when trying to run `mashtree` (1.4.6) with `*.msh` files as input. > looking at Mashtree.pm it seems that $outdir/tree.dnd.tmp...

Hi! Sorry for the hitchhiking. I also had trouble running `make_lastz_chains` on an HPC that runs PBS, likely due to some internal configuration of the HPC. After trial and error,...

> Hi @ohdongha, How much memory did you need for your mammalian-size genomes? I want to run it on a 3GB allotetraploid plant. I typically ask for 360 GB and...

> I just fixed the --continue arg usage. > If you'd like to rerun starting from a specified step, just call make_chains.py with --continue_arg $desired_step > You can manually fix...

> If you can put all data (chains, 2bit etc) on a download link where I can download and run it locally, I can check if this would potentially fix...

> I can provide the cleaned chains, if you want. Thanks, Michael. For this particular chain, I have already processed without running the `chainCleaner` step. Would it be possible to...

> I uploaded our x86_64 binary to https://github.com/hillerlab/make_lastz_chains/tree/main/HL_kent_binaries Would be great if you could test if this works on your system as well. Thanks, Michael. I tried on our server,...