allcools mcad
allcools mcad¶
Warning
This command is deprecated, please consider using allcools generate-dataset as the uniform method to generate methylation count matrix.
execute_command_and_return_markdown('allcools generate-mcad -h')
$ allcools generate-mcad -h
usage: allcools generate-mcad [-h] --allc_table ALLC_TABLE --bed_path BED_PATH
--output_prefix OUTPUT_PREFIX --mc_context
MC_CONTEXT [--cpu CPU] [--cutoff CUTOFF]
optional arguments:
-h, --help show this help message and exit
--cpu CPU Number of processes to use in parallel. (default: 1)
--cutoff CUTOFF Values smaller than cutoff will be stored as 0, which
reduces the file size. (default: 0.9)
required arguments:
--allc_table ALLC_TABLE
Contain all the ALLC file information in two tab-
separated columns: 1. file_uid, 2. file_path. No
header (default: None)
--bed_path BED_PATH Arbitrary genomic regions can be defined in one BED
file to count on. The fourth column of the BED file
should be unique id of the regions. (default: None)
--output_prefix OUTPUT_PREFIX
Output prefix of the MCAD, a suffix ".mcad" will be
added. (default: None)
--mc_context MC_CONTEXT
mC context pattern to extract from ALLC. Context
pattern follows IUPAC nucleotide code, e.g. N for
ATCG, H for ATC, Y for CT.Note that generate_mcad only
take one mC context (default: None)