Project management for cloud genomics: Glossary

Key Points

Data Tidiness

  • Metadata is key for you and others to be able to work with your data.

  • Tabular data needs to be structured to be able to work with it effectively.
Planning for NGS Projects

  • Data being sent to a sequencing center also needs to be structured so you can use it.

  • Raw sequencing data should be kept raw somewhere, so you can always go back to the original files.
Why of cloud computing

  • Cloud computing increases processing speed and efficiency
Logging onto the Cloud

  • You can use one set of log-in credentials for many instances

  • Logging off an instance is not the same as turning off an instance
Introducing the Shell

  • The shell gives you the ability to work more efficiently by using keyboard commands rather than a GUI.

  • Useful commands for navigating your file system include: ls, pwd, and cd.

  • Most commands take options (flags) which begin with a -.

  • Tab completion can reduce errors from mistyping and make work more efficient in the shell.

Glossary

accession
a unique identifier assigned to each sequence or set of sequences
categorical variable
Variables can be classified as categorical (aka, qualitative) or quantitative (aka, numerical). Categorical variables take on a fixed number of values that are names or labels.
cleaned data
data that has been manipulated post-collection to remove errors or inaccuracies, introduce desired formatting changes, or otherwise prepare the data for analysis
conditional formatting
formatting that is applied to a specific cell or range of cells depending on a set of criteria
CSV (comma separated values) format
a plain text file format in which values are separated by commas
factor
a variable that takes on a limited number of possible values (i.e. categorical data)
Gb
gigabyte of file storage or file size
Gbase
a gigabase represents one billion nucleic acid bases (Gbp may indicate one billion base pairs of nucleic acid)
headers
names at tops of columns that are descriptive about the column contents (sometimes optional)
metadata
data which describes other data
NGS
common acronym for “Next Generation Sequencing” currently being replaced by “High Throughput Sequencing”
null value
a value used to record observations missing from a dataset
observation
a single measurement or record of the object being recorded (e.g. the weight of a particular mouse)
plain text
unformatted text
quality assurance
any process which checks data for validity during entry
quality control
any process which removes problematic data from a dataset
raw data
data that has not been manipulated and represents actual recorded values
rich text
formatted text (e.g. text that appears bolded, colored or italicized)
string
a collection of characters (e.g. “thisisastring”)
TSV (tab separated values) format
a plain text file format in which values are separated by tabs
variable
a category of data being collected on the object being recorded (e.g. a mouse’s weight)