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lh3 / hickit

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
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Dip-c included ? #33

Closed Xparx closed 1 year ago

Xparx commented 1 year ago

Hello,

I'm trying to follow the instructions from the documentation but I get stopped at first line 

# Map Dip-C reads and extract contacts (skip if you use your own pipeline)
./seqtk mergepe read1.fq.gz read2.fq.gz | ./pre-dip-c - | bwa mem -5SP -p hs37d5.fa - | gzip > aln.sam.gz

It says I need dip-c. In the dip-c repository it said that a faster better version is included in hickit. If so; how do I use this version? If it's not included, dip-c is needed to be downloaded from the dip-c repo and can be used here?

Regards

lh3 commented 1 year ago

See README: pre-dip-c is from https://github.com/lh3/pre-pe

Xparx commented 1 year ago

Thank you for the quick response. Working through understanding the pipeline. All good for this. :fist_right:

lh3 commented 1 year ago

Good to know!