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