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dinhdiep / MONOD2

MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
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Missing allcpg directory in the repository #7

Open crotoc opened 5 years ago

crotoc commented 5 years ago

Hi dinhdiep, I am very interested in your great work and want to use your method to generate MHL for liver cancer. When running your script I found there are some missing in the examples. For example, in this command:

./scripts/bam2cghap.sh allcpg/cpg.small.txt.gz BAMfiles/Colon_primary_tumor_sept9_promoter.bam test

I can not find a allcpg directory in your repository. With out the file, I can't figure out the format and generate my own file that is compatible with the command.

And in this command,

./scripts/cghap2mhbs.sh results/HaploInfo/chr22.sub.hapInfo.txt example/N37_10_tissue_pooled.autosomes.RD10_80up.genomecov.bed 0.3 chr22

The results/HaploInfo/chr22.sub.hapInfo.txt is missing. I assume that this file is generated from one step of your script.

Can you help me address this problem? Thanks!

Honchkrow commented 5 years ago

The same problem. Can you provided these file? @dinhdiep

Thanks!

long692108 commented 4 years ago

The same problem. Can you provide me these files? @dinhdiep