$ allcools allc-to-bigwig -h
usage: allcools allc-to-bigwig [-h] --allc_path ALLC_PATH --output_prefix
OUTPUT_PREFIX [--bin_size BIN_SIZE]
--mc_contexts MC_CONTEXTS [MC_CONTEXTS ...]
--chrom_size_path CHROM_SIZE_PATH
[--strandness {split,both}]
optional arguments:
-h, --help show this help message and exit
--bin_size BIN_SIZE Bin size of the BigWig files. (default: 50)
--strandness {split,both}
What to do with strand information, possible values
are: 1. both: save +/- strand together in one file; 2.
split: save +/- strand into two separate files, with
suffix contain Watson (+) and Crick (-); 3. merge:
This will only merge the count on adjacent CpG in +/-
strands, only work for CpG like context. For non-CG
context, its the same as both. (default: both)
required arguments:
--allc_path ALLC_PATH
Path to 1 ALLC file (default: None)
--output_prefix OUTPUT_PREFIX
Path prefix of the output BigWig file. (default: None)
--mc_contexts MC_CONTEXTS [MC_CONTEXTS ...]
Space separated mC context patterns to extract from
ALLC. The context length should be the same as ALLC
file context. Context pattern follows IUPAC nucleotide
code, e.g. N for ATCG, H for ATC, Y for CT. (default:
None)
--chrom_size_path CHROM_SIZE_PATH
Path to UCSC chrom size file. This can be generated
from the genome fasta or downloaded via UCSC
fetchChromSizes tools. All ALLCools functions will
refer to this file whenever possible to check for
chromosome names and lengths, so it is crucial to use
a chrom size file consistent to the reference fasta
file ever since mapping. ALLCools functions will not
change or infer chromosome names. (default: None)
