DNase Hi-C

[kalavattam]

Hi, thank you for the great program.

Do you have any recommendations, advice, or considerations for using mHi-C with Hi-C datasets generated with the in situ DNase Hi-C protocol (which uses DNase I instead of restriction enzymes)?

[yezhengSTAT]

Hello, That is a great question. The mHi-C model should apply but the pipeline will need to be adjusted for DNase Hi-C protocol. Currently, mHiC uses the restriction enzyme cutting site to check if the read alignment position is valid (i.e., if the candidate alignment position is too far away from the enzyme cutting site) and the enzyme recognization pattern is used for rescuing chimeric reads (this function can be turned off). Therefore, you will probably need to customize the third step of the pipeline to make it run on DNase Hi-C data.

Hope it is helpful. ;)

Thanks, Ye

[dborgesr]

Just wanted to chime in and say i ran into the same problem while trying to run Micro-C data through the pipeline and see if you were able to get it running? If i get some free time i'll try to edit step three to allow no fragment files (need to edit the input parameter checking as well as the main loop to not check for fragment lenghts etc)