Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Effective genome size calculations seems to be incorrect. #76

Open
iromeo opened this issue Dec 3, 2018 · 1 comment
Open

Effective genome size calculations seems to be incorrect. #76

iromeo opened this issue Dec 3, 2018 · 1 comment
Assignees

Comments

@iromeo
Copy link
Contributor

iromeo commented Dec 3, 2018

Why do we calculate it using:

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.

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.

@iromeo
Copy link
Contributor Author

iromeo commented Dec 3, 2018

E.g. for mm9 we use 0.6860458146655941 and using DeepTools table it should be in 0.74..0.81 range depending on read length.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants
pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy