Target 16sRNAseq Analyse

• Legend Groups

  • (1) A1-A11 male aged 3d post-stroke
  • (2) B1-B16 female aged 3d post-stroke
  • (3) C1-C10 female aged BL FMT donor
  • (4) E1-E10 male aged BL FMT donor
  • (5) F1-F5 male young BL FMT donor
  • (6) G1-G6 FMT pre-antibiotics Male aged Batch I
  • (7) H1-H6 FMT pre-antibiotics Female aged Batch I
  • (8) I1-I6 FMT pre-antibiotics male young Batch II
  • (9) J1-J11 FMT pre-stroke Male aged
  • (10) K1-K15 FMT pre-stroke Female aged
  • (11) L1-L15 FMT pre-stroke Male young
  • (12) M1-M8 FMT post-stroke Male aged
  • (13) N1-N10 FMT post-stroke Female aged
  • (14) O1-O8 FMT post-stroke Male young

• Legend plots

  • PCA:
  • DGE:
  • Pathway-Analysis:
  • Bray-Curtis Distance:
  • Cladogram:
  • Bar-plot:

• I. Comparison Baseline and Stroke:

  • Baseline Gruppe 3 vs 4: PCA, DGE, Pathway-analysis, Bray-Curtis distance, Circle Cladogram

  • Stroke
    Gruppe 1 vs 2: PCA, DGE, Pathway-analysis, Bray-Curtis distance, Circle Cladogram

  • Baseline and Stroke Gruppe 1, 2, 3 and 4: PCA

• II. FMT Cohorts

  • Bar-plot of relative abundance of families/phyla:

    1. Groups: 3, 4, 5, 9, 10, and 11
    2. Groups: 6, 7, and 8

  • Comparison amongst FMT recipients

    1. Groups 9,10, and 11: PCA
    2. Groups 12,13, and 14: PCA

Standard processing

mamba activate /home/jhuang/miniconda3/envs/qiime1
mkdir fastqc_out
fastqc -t 4 raw_data/* -o fastqc_out/

R