Short-read Hi-C combined with CiFi

[dabitz]

Hi, great tool! Is it possible to combine both short-read Hi-C and CiFi data in a single run?

best
André

[wangyibin]

Hi, thank you for the helpful suggestion.

At present, C-Phasing does not natively support the simultaneous use of long-read and short-read data within a single run. Support for this functionality is planned for a future release.

As a workaround, users can currently combine the two data types by merging the pairs.pqs files generated from second- and third-generation sequencing data, and then running the pipeline on the merged file. For example:

example:

cphasing pairs-merge hic.pairs.pqs cifi.pairs.pqs -o merge.pairs.pqs 
cphasing pipeline -f unitigs.fasta -prs merge.pairs.pqs 

best
Yibin