Methylation

Methylation#

Quantification of methylation data#

We call the methylation data from a collection of IDAT file. The --sample_sheet_header_rows parameter govern the number of header rows in the sample sheet accompaning the IDAT file. By default, this number is 7

  • Resource Usage

    • time elapsed: 1550.12s

    • max vms_memory: 14.62GB

sos run pipeline/methylation_calling.ipynb sesame \
    --sample-sheet input_data/Methylation/xqtl_protocol_data_arrayMethylation_covariates.tsv  \
    --container containers/methylation.sif --sample_sheet_header_rows 0 --cwd output_rerun/methylation/
    
sos run pipeline/methylation_calling.ipynb sesame \
    --sample-sheet input_data/Methylation/xqtl_protocol_data_arrayMethylation_covariates.tsv  \
    --container containers/methylation.sif --sample_sheet_header_rows 0 --cwd output_rerun/methylation/ -q csg -c csg2.yml -J 1 &

Soft Impute to remove NA#

Many of the methylation matrix are filled with NA, softImputation are applied to the result.

  • Resource Usage

    • time elapsed: 143.58s

    • max vms_memory: 8.07GB

sos run pipeline/phenotype_formatting.ipynb bed_filter_na \
        --phenoFile output/methylation/xqtl_protocol_data_arrayMethylation_covariates.sesame.M.bed.gz \
        --cwd ./output/methylation/
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