Processing for Data_Marius_16S_2025

1. 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

2. Standard processing

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

3. R

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