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bioinformatics + data visualization

Learning Circos

Bioinformatics and Genome Analysis

Institut Pasteur Tunis Tunisia, December 10 – December 11, 2018

Download course materials
v2.00 6 Dec 2018
Download PDF slides
v2.00 6 Dec 2018

A 2- or 4-day practical mini-course in Circos, command-line parsing and scripting. This material is part of the Bioinformatics and Genome Analysis course held at the Institut Pasteur Tunis.

References

Circos resources

Guidelines for configuration files and data file organization.
A collection of tutorials.
A short introduction to Circos.

Perl tutorials

Perl tutorials
Perl tutorials
Perl tutorials

Command line tools

There are many command-line tools and these are some of the most useful. You should get to know each one very well.

field extractor
Extracts sections of each line based on number of characters, fields or delimiters
text processing and extraction tool
The basic function of awk is to search files for lines (or other units of text) that contain certain patterns. When a line matches one of the patterns, awk performs specified actions on that line. awk continues to process input lines in this way until it reaches the end of the input files.
line searcher
grep prints lines that contain a regular expression match for a pattern
combines lines from two files
Merges the lines of two sorted text files based on the presence of a common field. It is similar to the join operator used in relational databases but operating on text files.
simple file viewer
GNU less is a program similar to more, but which allows backward movement in the file as well as forward movement. Also, less does not have to read the entire input file before starting, so with large input files it starts up faster than text editors like vi.
joins files
Joins files horizontally (parallel merging) by outputting lines consisting of the sequentially corresponding lines of each file specified, separated by tabs, to the standard output. It is effectively the horizontal equivalent to the utility cat command which operates on the vertical plane of two or more files.
a stream editor
sed is a stream editor. A stream editor is used to perform basic text transformations on an input stream (a file or input from a pipeline). While in some ways similar to an editor which permits scripted edits (such as ed), sed works by making only one pass over the input(s), and is consequently more efficient. But it is sed’s ability to filter text in a pipeline which particularly distinguishes it from other types of editors.
line sorter
sort prints the lines of its input or concatenation of all files listed in its argument list in sorted order. Sorting is done based on one or more sort keys extracted from each line of input.
translate characters
Replaces or removes specific characters in its input data set
uniqe line extractor
Collapses identical lines to one and counts the number of runs of identical lines.
create commands from text
Builds and executes commands from standard input. It converts input from standard input into arguments to a command
Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA
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