Notebook 11/14/2014

Deleted all work from past few months! Cleaning up files and removed files in wrong directory!

Opportunity for a fresh start

Objectives

step up directory structure for study
setup docker for performing analysis

Directory structure



In [14]:

    
%%bash
tree -d ../









    



../
├── analysis
│   ├── bioinf
│   │   ├── genome_purity
│   │   ├── genome_structure
│   │   ├── sequence_homogeneity
│   │   └── sequence_purity
│   └── stats
├── bin
├── data
│   └── RM8375
│       ├── MiSeq
│       │   ├── bam
│       │   ├── fastq
│       │   └── vcf
│       ├── PGM
│       │   ├── bam
│       │   └── vcf
│       └── ref
├── dev
│   └── tmp
├── doc
└── src

22 directories

analysis - code for performing data analysis
1. bioinf - scripts for running bioinformatic pipelines
2. stats - code for statistical summary of pipeline results
bin - binaries for bioinformatic algorithms, note this may be included in the docker image
data - raw sequence data
dev - analysis playground
doc - general project documentation
src - source code for bioinformatic algorithms

Github repositories

analysis/bioinf
- genome_structure
- genome_purity
- sequence_purity
- sequence_homogenetiy

For each README.md file describing analysis approach and bash or ipython pipeline scripts



In [9]:

    
mv sequence* ../analysis/bioinf/

Approach download related repositories will create new directories for the three different applications and transfer related files to each.

TO DO

set up github repository
look into github annex for data
code for creating directories for other reference materials - use -p for creating parents and {A,B,C} for multiple subdirectories
vcf file for base quality score recalibration
work on PGM variant call script



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