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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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How can I set up enzyme_sites with enzyme DpnII? #52

Closed sunnycqcn closed 4 years ago

sunnycqcn commented 4 years ago

Hello, My Hi-C data was obtained using enzyme DpnII. However, AllHiC only has two enzyme options, such as -e : enzyme_sites (HindIII: AAGCTT; MboI: GATC). How can I set up the enzyme sites or I do not need set it? Thanks, Fuyou

tangerzhang commented 4 years ago

Hi Fuyou, You can use the restriction sites directly, e.g. -e GATC

sunnycqcn commented 4 years ago

Hello, Can I use GATC replace MBOI at this step? PreprocessSAMs.pl sample.bwa_aln.sam draft.asm.fasta MBOI Thanks, Fuyou

tangerzhang commented 4 years ago

Yes, as long as this script was downloaded from ALLHiC package rather than LACHESIS package.