How to generate cpg.1m.txt file for GRCh38?

tanlongzhi / dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data

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How to generate cpg.1m.txt file for GRCh38? #46

Closed AIBio closed 2 years ago

AIBio commented 2 years ago

Hi Longzhi,

I want to apply Hg38 version genome to analyze Dip-C data. But I cannot find the suitable cpg.1m.txt file or cpg.20k.txt files for Hg38. Could you teach me how to generate these files?

Hanwen 2022/05/27

tanlongzhi commented 2 years ago

Hi Hanwen,

You can use the following line:

scripts/cpg.sh hg38.fa 1000000 > hg38.cpg.1m.txt

Please use the same FASTA file that you used for mapping, so that chromosome names match perfectly.

Best, Tan

AIBio commented 2 years ago

Hi Hanwen,

You can use the following line:
scripts/cpg.sh hg38.fa 1000000 > hg38.cpg.1m.txt
Please use the same FASTA file that you used for mapping, so that chromosome names match perfectly.

Best, Tan

Got it, thank you !!!