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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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Do you recommend bwa mem with or without the -5 option for aligning normal hi-c data #23

Closed jelber2 closed 4 years ago

jelber2 commented 4 years ago

I noticed that in https://github.com/lh3/hickit/blob/e8d87c4e2bb8cef1789098eff64501339db97e0a/README.md,

Aligning Hi-C reads

If have normal Hi-C reads, you can align directly with bwa-mem:

bwa mem hs37d5.fa read1.fq.gz read2.fq.gz | gzip > aln.sam.gz

Is there some reason not to use the -5 option for aligning normal hi-c read pairs?

lh3 commented 4 years ago

To hickit, this option doesn't matter.

jelber2 commented 4 years ago

Okay, thank you very much for the prompt response!