Glossary

File formats

yaml: Language to serialize objects. Used in the CGAT testing framework. (YAML).
bam: Format to store genomic alignments in a compressed format.

bed File containing genomic intervals. (BED).

gtf General transfer format. Format to store genes and transcripts.

bigwig: Compressed format for displaying numerical values across genomic ranges (BIGWIG).
fasta: Sequence format.
wiggle: Format for displaying numerical values across genomic ranges (Wiggle).
psl: Genomic alignment format. The format is described in detail

gdl: gdl
tsv: Tab separated values. In these tables, records are separated by new-line characters and fields by tab characters. Lines with comments are started by the # character and are ignored. The first uncommented line should contain the column headers. For example:
# This is a comment: gene_id length gene1 1000 gene2 2000 # Another comment
svg: pass
edge list: pass
fastq: Sequence format containing quality scores, more background is

reference files for testing scripts.

graph graph

graph graph

goslim pass

fastq: pass
tss: Transcription start site
production pipeline: A pipeline that performs common tasks on a certain type of data. The idea of a production pipeline is to provide common preprocessing of data and a first look. A project pipeline might then take data from one or more production pipeline to glean biological insight.
project pipeline: A pipeline that is project specific. Usually code is developed
first inside a project pipeline. When it becomes generally: useful, it may be refactored into a production pipeline.
stdin: Unix standard input. Most CGAT tools read data from stdin.
stdout: Unix standard output. Most CGAT tools output data to stdout.
stderr: Unix standard error. This is where errors go.
loglevel: Verbosity of logging information. The logging level can be determined by the --verbose option. A

level of 0 means no logging output, while 1 is information messages only, while 2 outputs also debugging information.