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def effective_genome_fraction(genome, chrom_sizes_path):
"""From MACS2 documentation:
The default hs 2.7e9 is recommended for UCSC human hg18 assembly.
Here are all precompiled parameters for effective genome size:
hs: 2.7e9
mm: 1.87e9
ce: 9e7
dm: 1.2e8"""
chrom_length = int(run([['cat', chrom_sizes_path],
['grep', '-v', 'chr_'],
['awk', '{ L+=$2 } END { print L }']
])[0].decode('utf-8').strip())
if genome.startswith('mm'):
size = 1.87e9
elif genome.startswith('hg'):
size = 2.7e9
else:
raise Exception('Unknown species {}'.format(genome))
return size / chrom_length
According to SICER docs
This can be calculated using the software describe inThe uniqueome: a mappability resource for short-tag sequencing by Ryan Koehler, Hadar Issac, Nicole Cloonan, and Sean M. Grimmond, Bioinformatics (2011) 27 (2): 272-274.
Sicer galaxy plugin:
Effective Genome as fraction of the genome size. It depends on read length.
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Why do we calculate it using:
According to SICER docs
Sicer galaxy plugin:
According to DeepTools - it also depends on read size, see https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html.
The above impl doesn't depend on reads size.
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