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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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beta2bed warning - incomatible (sic) with current genome reference #67

Open cb4github opened 2 months ago

cb4github commented 2 months ago

Dear All,

Thanks for your efforts.

Steps follow. # Clone git clone https://github.com/nloyfer/wgbs_tools.git cd wgbs_tools

# compile python setup.py module load anaconda3/5.1.0 gcc/8.5.0 samtools/1.16.1 htslib/1.19 export PATH=$PATH:$PWD cd wgbstools init_genome --force --no_default --debug --threads 19 hg38 wget --directory-prefix=data ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5652nnn/GSM5652231/suppl/GSM5652231_Cerebellum-Neuron-Z000000TB.hg38.beta mkdir output wgbstools beta2bed --outpath output/GSM5652231_Cerebellum-Neuron-Z000000TB.hg38.bed --genome hg38 data/GSM5652231_Cerebellum-Neuron-Z000000TB.hg38.beta

Output follows. [wt beta] WARNING: beta file size (29,401,795 sites) incomatible with current genome reference (1,822 sites)

Also, the bed file apparently is successfully created. $ls -lt output
total 20
-rw-r--r-- 1 18740 Apr 5 15:02 GSM5652231_Cerebellum-Neuron-Z000000TB.hg38.bed

Please advise. Thanks.

Best, CB