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Hi, Maybe I was not clear. (1) Is there any way to use allhic without using a reference? (2) what would you suggest to use as a reference for a...

Yes, thanks we are now using a monoploid assembly. However, we followed the issue https://github.com/tangerzhang/ALLHiC/issues/75 and we decided to (1) used the ALLHiC_corrector and (2) filter hi-C reads using Hi-C...

Hi, The problem was the group assignment to the homologous groups. We divided the contigs into the 12 homologous chromosomes divided by two, thus 24 (chri_1, chri_2) because we are...

Thanks for your answer I am going to try, is it possible to give the reads in fasta format to RATTLE?

Hi, it did not work. I tried with the fasta and the fastq, but in both cases, it shows an error `terminate called after throwing an instance of 'std::bad_alloc`. Is...