jiangshan529

same question, please let me know if they respond or if you figure it out.

> Hi, dear authors, I have used coolpup a lot previously, but recently it has some problem(maybe a version problem of some packages): coolpup.py aa.cool bb.bed --outname cc.txt --flank 250000...

> Oh I see what you mean. I don't know who uploaded the strawC version. @nchernia @zozo123 @cwenger ? Hi, now hic-straw is really hard to be installed. when I...

> It means that these rows (bins) had to be removed during normalization. You should not see any NaN (Not a Number) in raw (un-normalized) map. Hi, thanks for your...

> Are you using oe (observed over expected)? If so, float numbers should not surprise you. On Tuesday, 15 November 2022 at 02:40:34 pm AEDT, jiangshan529 ***@***.***> wrote: It means...

> Where does this hic file come from? Is it a (weighted) combination of several maps? On Tuesday, 15 November 2022 at 02:53:12 pm AEDT, jiangshan529 ***@***.***> wrote: Are you...

> By the way, have you tried using dump command in juicer tools? Does it produce identical results (to straw)? On Tuesday, 15 November 2022 at 03:02:28 pm AEDT, jiangshan529...

> Have you downloaded juicer_tools.jar?If so, do java -jar juicer_tools.jar or/and java -jar juicer_tools.jar dump to see the usage. On Tuesday, 15 November 2022 at 03:20:17 pm AEDT, jiangshan529 ***@***.***>...

> Apologies - if there is indeed a bug (different outputs from straw vs dump), then we should indeed discuss it here. Can you share the commands you used for...

> Is this specific to this region or genome wide? Also have you looked at the contact maps themselves and do they noticably differ near the diagonal? It's genome-wide. And...