U.S. Department of EnergyOffice of Scientific and Technical Information
Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity
Abstract
This record contains a list of Snakemake rules (Snakefile) to process a raw *.fastq.gz (from GEO record: GSE281607) using Cutadapt, map a processed *.fastq file using Bowtie, convert mapped reads to *.bed files using Samtools and Bedtools, and count the occurance of each Bacteriodes fragilis str NCTC 9343 genome position anywhere in a mapped read and as the 3' end of a mapped read using Bedtools. It further contains *ebwt files to assist with Bowtie mapping, *genome file to be used with Bedtools, a *.fasta file (useful to regenerate *ebwt files), and the completely processed *bed and *txt read files (generated by Snakemake and R) as references. In addition, a *.pdb file is included and represents the predicted interaction between UpeY and UpaZ.
- Authors:
-
- GLBRC - University of Wisconsin
- Publication Date:
- DOE Contract Number:
- SC0018409
- Research Org.:
- Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 3001541
- DOI:
- https://doi.org/10.5281/zenodo.14110861
Citation Formats
Landick, Robert. Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity. United States: N. p., 2024.
Web. doi:10.5281/zenodo.14110861.
Landick, Robert. Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity. United States. doi:https://doi.org/10.5281/zenodo.14110861
Landick, Robert. 2024.
"Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity". United States. doi:https://doi.org/10.5281/zenodo.14110861. https://www.osti.gov/servlets/purl/3001541. Pub date:Fri Jun 21 00:00:00 EDT 2024
@article{osti_3001541,
title = {Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity},
author = {Landick, Robert},
abstractNote = {This record contains a list of Snakemake rules (Snakefile) to process a raw *.fastq.gz (from GEO record: GSE281607) using Cutadapt, map a processed *.fastq file using Bowtie, convert mapped reads to *.bed files using Samtools and Bedtools, and count the occurance of each Bacteriodes fragilis str NCTC 9343 genome position anywhere in a mapped read and as the 3' end of a mapped read using Bedtools. It further contains *ebwt files to assist with Bowtie mapping, *genome file to be used with Bedtools, a *.fasta file (useful to regenerate *ebwt files), and the completely processed *bed and *txt read files (generated by Snakemake and R) as references. In addition, a *.pdb file is included and represents the predicted interaction between UpeY and UpaZ.},
doi = {10.5281/zenodo.14110861},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Fri Jun 21 00:00:00 EDT 2024},
month = {Fri Jun 21 00:00:00 EDT 2024}
}