Xiangyu Pan

Another question; should we implemented picard tools to remove duplicates reads caused by PCR after bwa alignment?

Thanks, I will follow your suggestion. And one more quenstion, whether this tool could identify ecDNA (Extrachromosomal DNA) not only eccDNA？ And are there any tools to visualise Circle-Map results?...

Thanks for immediately replying. And one more thing I want to make sure about the results, each rows of files meant they could fomed an eccDNA individually, or combination of...

I have a same problem but more worse, I have eight sample bam files without a clear @RG header, and their peaks files obtained by executing getPeaks() function having different...

whether it would be okay for the pre-porcessing of bam files, we just deduplicate the bulk RNA-seq bam.

Hi Tan, I found the chromosome name of my data had 'chr', so I modified the source data of `reg3.py` to make it possible to remove the CN regions as...

> I have figrued it out, I found the wrong `.3dg` files were used as input. When I used the `.20k.${rep}.dip-c.3dg` files, produced by `hickit_3dg_to_3dg_rescale_unit.sh`, to run `$DIP_C reg3`, the...

Hi Tan, Recently, I use `dip-c` for subsequent analysis on the GM12878 data. I found the structure reconstruction were different by aligning with different version of reference (hg38 and/or hg19)....