Matrix Assembly

BSBolt AggregrateMatrix takes a list of CGmap files, compressed or uncompressed, and assembles a consensus methylation matrix. Methylated sites that pass a read depth threshold and are present in a set proportion of samples are included in the matrix.

BSBolt AggregateMatrix Commands

bsbolt AggregateMatrix -F {file1.CGmap,file2.CGmap,...} -O {output_matrix.txt}

-h, --help              show this help message and exit

Options:
  -F File,File,.        comma separated list of CGmap files
                        or path to text file with list of line separated CGmap files
  -S Str,Str,.          comma separated list of samples labels. If sample labels are not provided sample labels
                        are extracted from CGmap files. Can also pass path to txt for line separated sample labels.
  -min-coverage Int     minimum site read depth coverage [10]
  -min-sample Float     proportion of samples that must have a valid site (above minimum coverage threshold) [0.8]
  -O File               Aggregate matrix output path
  -CG                   Only output CG sites
  -verbose              Verbose aggregation
  -t Int                Number of threads to use when assembling matrix [1]
  -count                Output a count matrix with count of methylated cytosines and total observed cytosines

Aggregate Matrix Default Settings

python3 -m bsbolt AggregateMatrix -F cgmap_1,cgmap_2,cgmap_3 -O ~/test_matrix.txt

Aggregate Matrix Default Settings - File List

python3 -m bsbolt AggregateMatrix -F cgmap_file_list.txt -O ~/test_matrix.txt

Aggregate Matrix Default Settings - File List, Sample Labels, Verbose

python3 -m bsbolt AggregateMatrix -F cgmap_file_list.txt -S sample1,sample2,sample3 -O ~/test_matrix.txt -verbose