STENO Phylogenomics, Metabolomics, Transcriptomics, Metatranscriptomics

Growth data from in vitro experiments

Scripts

Main growth data in THB /code/scripts/R
Growth data in ASM /code/scripts/R

Data

Growth curve data /GrowthData

Phylogenomics

Scripts

Phylogenomics by A. Chase and A. Oliver
contact for info about scripts for phylogenomics
compare accessory gene content: /code/scripts/R
look at distrubution of genes across Steno strains /code/scripts/R

Data

153 strain tree using 21 marker genes: /data/processed/genome/phylogenetic/Old_153strains
core genome tree (74 strains, 95% AAI clusters): /data/processed/genome/phylogenetic/newtree_alex

Metabolomics

Scripts

PCOA and volcano plots of metabolomics data in R: /code/scripts/R

Data

metabolomics data from WCMC: /data/metabolomics

Transcriptomics

Scripts

Pipeline for data from raw to alignments and HT-Seq Count hits /code/scripts/Transcriptome
transcriptome analyses in R, including DGE /code/scripts/R/trancriptome_R_stuff

Data

raw data = https://www.ncbi.nlm.nih.gov/bioproject/?term=GSE121347
BAM alignments to FLR19 genome: /data/processed/bowtie2
HT-Seq output: /data/processed/HTSeq

Metranscriptomics

Scripts

quality filter data in linux environment: /code/scripts/Metatranscriptome
align to non-Steno CF database: /code/scripts/Metatranscriptome
align left-overs to Steno pan-genome:/code/scripts/Metatranscriptome
look at gene alignments: /code/scripts/Metatranscriptome
look at gene hits in sputum E and F: /code/scripts/Metatranscriptome

Data

meta transcriptomes from Marvin Whiteley's Lab: https://www.pnas.org/content/115/22/E5125.short
alignment to Steno pan-genome: /data/processed/CFdata/Whiteley/new_aligned