Quentin Szabo et al. ,TADs are 3D structural units of higher-order chromosome organization in Drosophila.Sci. Adv.4,eaar8082(2018).DOI:10.1126/sciadv.aar8082
- Hoe Zi Onn, 111753229
- Han-Cheng Guan, 112753134
- Hao-Yun Hsieh, 112753120
To use our pre-configured environment for the first time (assuming you have git
& docker
installed):
git clone https://github.com/1121-NCCUBionf/finalproject-group1.git
cd finalproject-group1
docker volume create project-data
docker build -t project-env .
docker run -v project-data:/project-data -it project-env
- store your data in
project-data
docker volume - and you can access your data in
/project-data
directory inside the container
- Our presentation, 1121_bioinformatics_FP_group1.pdf
- Any related document for the project
- A note for the development
downloadable data are not included in this repository see here for more information.
Data | Source | Format | Size | Description |
---|---|---|---|---|
Raw Data | NCBI GSE99107 | fastq |
~ 250 GB (compressed) | 6 samples |
Reference Genome | UCSC dm6 | fasta |
147 MB | 2014 |
Genome Index | from bowtie2 |
bt2 |
- | - |
- Packages we use
- original packages in the paper
- None
- additional packages we found
- original packages in the paper
- scripts
- for downloading raw fastq data
- for running
fanc
example pipeline - for running
fanc
pipeline with our data - for splitting fastq files into smaller chunks
- handy
Makefile
to copy file between host and container
- Which part of the paper do we reproduce?
- Hi-C data processing
- Hi-C contact map visualization
- Improvement or change in our package?
- we use
dm6
genome instead ofdm3
- we use
- see packages/tools we use here.