/mgen

Primary LanguageR

Haruo Suzuki
Last Update: 2016-03-22

Mycoplasma genitalium (mgen) Project

Project started 2015-11-15.

A complete genome of Mycoplasma genitalium G37 was retrieved from the NCBI FTP site. R language was used to assess genome features (length, base composition, and GC content of the DNA sequence, and local variation in GC content and skew).

Project directories

mgen/
 README.md: project documentation 
 data/: contains sequence data in FASTA format
 scripts/: contains R and Shell scripts
 analysis/: contains results of data analyses

Data

FASTA format sequences of Nucleic Acids (GCF_000027325.1_ASM2732v1_genomic.fna.gz) and Amino Acids (GCF_000027325.1_ASM2732v1_protein.faa.gz) downloaded on 2016-01-22 from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000027325.1_ASM2732v1/ into data/:

# MD5 Checksums
MD5 (data/GCF_000027325.1_ASM2732v1_genomic.fna.gz) = 456f609c24abab75d4d593b5c92bd631
MD5 (data/GCF_000027325.1_ASM2732v1_protein.faa.gz) = 02805a93d8dc783967e0a8fdb4511af5

Scripts

The shell script scripts/run.sh automatically carries out the entire steps: creating subdirectories, downloading data files, and running the R scripts scripts/my_analysis.R that calculates length and base composition of a DNA sequence, and scripts/my_sliding_window.R that generates sliding window plots of GC content and GC skew (analysis/Rplots_sliding_window.pdf).

Let's run the driver script in the project's main directory mgen/ with:

bash scripts/run.sh > log.txt 2>&1 &

Inspecting Data

cd data/
ls -lh
# Working with Gzipped Compressed Files using gzcat, zgrep, and zless
gzcat *.fna.gz | head -n 2
zgrep -c '^>' *.gz
zless *.faa.gz

Updates

  • 2016-01-22

  • Downloaded data from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000027325.1_ASM2732v1/

  • 2016-01-11

  • Created the R script scripts/my_sliding_window.R

  • 2015-12-04

  • Downloaded data from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000027325.1_ASM2732v1/

  • 2015-11-15

  • Created the project directory using mkdir -p mgen/{data,scripts,analysis}

  • Downloaded data from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/

  • Created the shell script scripts/run.sh and R script scripts/my_analysis.R

References