week 10 update

README.md

@@ -28,35 +28,45 @@ In this project I will be developing scripts to generate a phylogenetic tree usi
 - Week 3: Quality check data and install required programs
 - Week 4: Trim adapters and filter low quality sequences
 - Week 5: Exploration in using a remote computer
-- Week 6: Start assembling filtered reads into contigs
-- Week 7 (planned): Finish assembling filtered reads into contigs
-- Week 8 (planned): Merge the loci containing more than one contigs
+- Week 6: Remove duplicates from PCR.
+- Week 7: Parse reads to each locus.
+- Week 8: Get started assembling filtered reads into contigs.
+- Week 9: Problem solving using Trinity and Bowtie
+- Week 10: Visualize and present project
 
 ### Details
 Project Directory Location:
 
-- Local:  `/Users/calderatta/Desktop/FISH\ 546\ -\ Bioinformatics/project/`
+- Local:  `/Users/calderatta/Desktop/FISH546_Bioinformatics/project/`
 - GitHub: `/Users/calderatta/Documents/GitHub/calder-exon-capture/`
 
 Contents:
-
 - `analysis/` Results from various analyses.
+   - `bowtie-test/` Files for trouble-shooting using bowtie (2018-12-03)
    - `fastqc/` Output from fastqc (2018-10-23)
    - `merge/`  Output from cat (2018-10-26)(Empty on GitHub)
-   - `preads/` Output from preads (In Progress)(Empty on GitHub)
+   - `preads-bandp/` Output from bandp (2018-11-15)(Empty on GitHub)
+   - `preads-rmrep/` Output from rmrep (2018-11-05)(Empty on GitHub)
    - `trimgalore/`  Output from trimgalore (2018-10-26)
+   - `trinity/` Output from Trinity (In progress...)
 - `data/` Contains 28 source .fastq files. (Empty on GitHub)
 - `kuang-et-al-2018/` Contains publication and associated supplamentary material.
+- `markers/` Contains reference markers for data.
 - `notebooks/` Jupyter notebooks associated with this project.
-    - `main.ipynb`
+    - `environmental_variables.ipynb`
+    - `installation_Trinity.ipynb`
     - `installation.ipynb`
+    - `main.ipynb`
+    - `Tmux-Jupyter.md`
+- `presentation/` Course presentation material. (Empty on GitHub)
 - `README.md` You Are Here! Contains details about project, organization, and history.
-- `scripts/` (Empty)
-
+- `screenshots/`
+- `scripts/` Contains scripts used for analyses and pipeline for using them.
+- `scripts-outdated/` Outdated scripts that are replaced in `scripts/`.
+- `week-6-quiz/`
 
 ### History
 
-
 2018-10-18
 - Started README.md. Local directory contains `analysis/` (empty), `calder-exon-capture.ipynb`, `data/`, `kuang-et-al-2018/`, `README.md`, `scripts/` (empty). GitHub directory contains `calder-exon-capture.ipynb`, `README.md`.
 
@@ -74,3 +84,21 @@ Contents:
 
 2018-11-02
 - Renamed `trimgalore` output and moved to `kuang-et-al-2018/scripts-old/preads_script/`. Created `kuang-et-al-2018/kuang-et-al-2018-notes.md`
+
+2018-11-08
+- `week-6-quiz` added to GitHub.
+
+2018-11-14
+- Uploaded `preads-script/` to GitHub to run samples on MOX. Created `notebooks/environmental-variables.ipynb`
+
+2018-11-26
+- Scripts in `kuang-et-al-2018/scripts-old` moved to `scripts/`. Created `notebooks/Tmux-Jupyter.md`
+
+2018-11-27
+- Troubleshooting issues with Trinity. `notebooks/main.ipynb` updated. Created `notebooks/installation_Trinity.ipynb`
+
+2018-11-29
+- Added `screenshots/`, `presentation/`.
+
+2018-12-03
+- Problem scripts identified as outdated moved from `scripts/` to new diectory `scripts-outdated/`.