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dinhdiep / MONOD2

MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
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Extracting methylation haplotypes from sequence alignment files #10

Open meb326 opened 5 years ago

meb326 commented 5 years ago

Hi dinhdiep,

I'm very interested in your work and want to conduct methylation haplotype analysis on my bisulfite sequencing data. I am having trouble generating CpG haplotype files using your code. When I try the test example: ./scripts/bam2cghap.sh allcpg/cpg.small.txt.gz BAMfiles/Colon_primary_tumor_sept9_promoter.bam test

I get this error for many lines: Use of uninitialized value $ref_seq in concatenation (.) or string at bin/getHaplo_PE_cgOnly.pl line 161, line 28.

Could you help me to get this to work? I would really appreciate it.

long692108 commented 4 years ago

Hi dinhdiep,

I'm very interested in your work and want to conduct methylation haplotype analysis on my bisulfite sequencing data. I am having trouble generating CpG haplotype files using your code. When I try the test example: ./scripts/bam2cghap.sh allcpg/cpg.small.txt.gz BAMfiles/Colon_primary_tumor_sept9_promoter.bam test

I get this error for many lines: Use of uninitialized value $ref_seq in concatenation (.) or string at bin/getHaplo_PE_cgOnly.pl line 161, line 28.

Could you help me to get this to work? I would really appreciate it.

long692108 commented 4 years ago

I am also interested in this work. Did you have solve this problem?

kythol commented 1 year ago

I have the same error