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dnascenttools

Set of scripts to process files produced by DNAscent

https://github.com/dnareplicationlab/dnascenttools

Science Score: 44.0%

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  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Scientific vocabulary similarity
    Low similarity (3.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Set of scripts to process files produced by DNAscent

Basic Info
  • Host: GitHub
  • Owner: DNAReplicationLab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 297 KB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

DNAscentTools

Set of scripts to process files produced by DNAscent.

Convert DNAscent detect to modBAM

Base modification probabilities can be added to BAM files using optional tags. Scripts here use a detect file and the corresponding reference genome as input and produce a BAM file, with probabilities of thymidine modification along each read specified using tags.

Please look at rundetectto_modBAM.sh for an example on how to perform a detect to modBAM conversion for different versions of DNAscent detect.

Owner

  • Login: DNAReplicationLab
  • Kind: user

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: DNAscentTools
message: >-
  If you use the software, please cite the
  peer-reviewed, published paper or a preprint,
  whichever is later, if/when it appears. Till then,
  please cite the software using these metadata.
type: software
authors:
  - given-names: Sathish
    family-names: Thiyagarajan
    email: mailboxofsat@gmail.com
    affiliation: Earlham Institute
    orcid: 'https://orcid.org/0000-0001-8545-8886'
  - orcid: 'https://orcid.org/0000-0003-2001-076X'
    affiliation: Earlham Institute
    email: Conrad.Nieduszynski@earlham.ac.uk
    given-names: Conrad
    family-names: Nieduszynski

GitHub Events

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Dependencies

requirements.txt pypi
  • modbampy ==0.5.4
  • numpy ==1.22.3
  • pysam ==0.19.1