MeiyuanJi

Hello, I was wondering if polca takes aligned BAM file? I already run the sequence alignment, want to directly input polca and only run for polishing steps. Many thanks. Best,...

Hi, I am using POLCA for genome polishing by taking the illumina paired end reads. I have in total 8 files (4 for forward reads; 4 for reverse reads). I...

Hi, I find the paper and the script is very useful. However, I didn't find any detail about how to normalize data before module detection. So, you just used the...

Hi, I am aware of that the ArchR package was developed primarily for the analysis of large scale scATAC-seq. Just out of curiosity, if this package is appropriate for the...

Hi, I use bwa to align paired-end reads to the reference genome. There are some cases, when the reads are labeled as paired alignment, and in the BAM file, only...

calling subcompartment for one sample with no replicates

5

Hi, I am wondering if I can call subcompartments for one sample only (no assignment of --diffdir) after running --pcatype "cis" and "select". I see in the paper, it used...

optimal resolution for compartment call

2

Hello, I noticed that when different resolution used, the compartment results may change. Is there any standard to help decide an optimal value for binsize? I attached some tests using...