sim3C
sim3C copied to clipboard
cerebis
Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
I would like to report two bugs. **WGS strandedness bug:** The first has to do with the strandedness of WGS reads. At this [line](https://github.com/cerebis/sim3C/blob/e58f5fb30b7e8b930db3df04ffed3db1ca9f2872/sim3C/community.py#L165) of code, it should be: `ss...
Currently, many simulation options are an all-or-nothing operation that affect the entire community. Adding these are annotations within the community definition would provide valuable fine-grained control. ## Example Simulations that...
The format used to define a community is presently a simple flat table. This approach incurs a great deal of duplicated information, and a cleaner approach would be a to...
An oversight has been discovered in the simulation of WGS pairs. Despite the possibility that real WGS pairs can span neighbouring contigs when occurring at contig-ends, during simulation in sim3C,...
Hi! I've spent some time debugging why sim3C seems to give too many read pairs where one read is at the end of a chromosome and the other at the...
Hello sim3C developers, This is not an issue. I would to know if sim3C can take pairs of genomic coordinates for which quimeric reads are also simulated. Many thanks Jorge
I've been having some trouble simulating HiC reads, and after an hour of troubleshooting I think I've identified the issue. This is the command I've been running, and the error...
Just realized that if a chromosome is defined as being in more than one copy, there is no possibility that it will interact with its twin(s). The probability draws are...
Real data from the S.stipitis genome demonstrates the characteristic X modulation of _trans_ interactions. This pattern is theorised to be due to spatial organisation of chromosomes. In particular, the collective...