Yanchun Zhang

Much lower reads quality than Guppy

3

Hi, I run bonito with 9.4.1_sup model on a R9 datasets while got really low reads quality(median 5) than I got from guppy (median 10). Is there anything wrong with...

Load local file so slow

1

Hi, I tryied those codes in Jupyter python as below: from higlass.client import View, Track from higlass.tilesets import cooler import higlass ts1 = cooler('4DNFI2A4OBS9.mcool') tr1 = Track('heatmap', tileset=ts1) view1 =...

Much higher reads quality by megalodon than Guppy

2

Hi, I found a very confusing result that when I run megalodon and guppy on the same datasets, the resulting reads quality in the summary file are largely higher in...

Hi, I saw from your lab's new published paper(https://www.biorxiv.org/content/10.1101/2020.02.26.966697v1.full) that "First, we identified 58,988 and 49,258 loops in SCABER and SW780 cells respectively (prob>0.8). Then by **using the probability score...

Hi, I would like to build a database including mouse genome, so could you please tell me the parameters used to build the available databases in https://benlangmead.github.io/aws-indexes/k2? I want to...

[help wanted] cannot use multi-cores when dealing with genlight

3

Hi, I have a data set of about 2600 individuals and 150, 000 SNPs for each individual. When I run read.PLINK or glPCA with parameter [parallel = require("parallel" )] on...

Normalized contact value?

7

Hi, do you calculate a normalized contact value in the final bed files? I checked the file but didn't see it. Just like the normalized value in Hi-C contact map....

Hi, When I run hichipper I set my own R path with conda and I installed the GenomicRanges library in my R. But when I run it, always got the...

Error when run chess_extract

3

Hi, I always got this error recently when run the chess_extarct command: do you have any idea about this error? Traceback (most recent call last): File "/home/ch220811/.local/bin/chess", line 585, in...