Liz Ing-Simmons

FWIW, I tried the `py3` branch out on my data and it seems to work well. I didn't run the python 2 version to compare though. The only thing I...

Hi, sorry for not providing more information! I'm running on Linux (CentOS 7). I'm running TOBIAS through Snakemake, and the Snakemake jobs end without producing any output files apart from...

Hi, after some further investigation, I think I figured it out. The processes ran fine outside of Snakemake/the job submission system, or if I gave the jobs more memory. I...

When you ran `chess sim`, you must have specified either `--background-regions` or `--background-query`. Using these options means that CHESS will calculate a z-score and corresponding p-value for the significance of...

If you can run CHESS successfully on the sample data, then I think this is likely an issue with your input data and not with CHESS itself. You could try...

Hi, this looks like the same issue as encountered here: https://github.com/vaquerizaslab/chess/issues/25 You can try the suggested solutions there. If those don't work, I would need access to a sample of...

Hi Lucía, The way the comparison across species was carried out in the paper was by using the syntenic regions in bedpe format as the input pairs file for `chess...

Since the syntenic regions likely have different sizes in the different species and the change in size may not be even across the region, I would probably start by taking...

Hi, and thanks for the question. We are aware of the preprint and are drafting a detailed response to it. With appropriate parameters and thresholds, the CHESS output can be...

Hello, Our preprint is available online now: https://www.biorxiv.org/content/10.1101/2021.10.18.464422v1 We've also updated the CHESS docs and FAQ with some additional guidance on best practices for using CHESS. I hope that clears...