Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity

Dataset · Fri Jun 21 04:00:00 EDT 2024

DOI:https://doi.org/10.5281/zenodo.14110861· OSTI ID:3001541

Landick, Robert ^[1]

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1. GLBRC - University of Wisconsin

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.

• Research Organization: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER)
• DOE Contract Number: SC0018409
• OSTI ID: 3001541
• Country of Publication: United States
• Language: English