Centers and Institutes
Published November 18, 2024 | Version v1
Software Metadata-only

[Scripts for] Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity

Creators

  • 1. University of Wisconsin–Madison
  • 2. University of Chicago

Description

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.

Additional details

Identifiers

DOI
10.5281/zenodo.14110861
Other
oai:uchicago.tind.io:14333

Related works

Is cited by
10.1038/s41467-024-55215-9 (DOI)
Is supplemented by
10.5281/zenodo.14110861 (DOI)

Funding

National Institutes of Health
R01 GM038660
U.S. Department of Agriculture
Hatch WIS05004
National Institutes of Health
R01 AI093771
University of Chicago
Office of Science, Department of Energy
Biological and Environmental Research Program Great Lakes Bioenergy Research Center
National Institutes of Health
Predoctoral Training Program in Genetics
National Institutes of Health
Biotechnology Training Grant
National Institutes of Health
Biotechnology Training Grant
National Institutes of Health
F31 Graduate Fellowship
University of Wisconsin–Madison
SciMed Graduate Research Scholars Fellowship

UChicago Information

Division(s)
Biological Sciences Division
Department(s)
Microbiology
Center(s) or Institute(s)
Duchossois Family Institute