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rr1859 / R.4Cker

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reduced genome and enz_file #36

Open nagoue opened 7 years ago

nagoue commented 7 years ago

Hi Ramya, I come back to you with questionning about the reduced genome that is now included in the createR4CkerObject function. In a previous version of your package, the enz_file was not required. Could you comment and that point? My concern is that there is basically 2 ways to conduct the mapping: your way i.e. mapping experiment directly on the reduced genome and the second which consist of first mapping experiment on full genome and filter it to the reduced genome. The last strategy is the one I have adopted and I am worry about the consequence of this "enz_file" fork in your package. Could you please add either the mm10_hindiii_flanking_sequences_25_unique.fa file or the enz_file to you data folder so that one can reproduce your example experiments? Thank you, Nadia

rr1859 commented 7 years ago

Hi, The reason I added it was to check the QC of the 4C samples. One of the criteria is to have >40% coverage in the region surrounding the bait. You can substitute this with a file containing the fragments for your primary restriction enzyme.

rr1859 commented 7 years ago

And yes I can add the enz_file to the data folder.

nagoue commented 7 years ago

Hi Ramya, Thank you for the explanation. Thank you for putting the enz_file from your examples. Best,

rr1859 commented 7 years ago

mm10_hindiii_flanking_sites_25_unique_2.bed.gz