plastid.bin.make_wiggle module¶
Create genome browser tracks from read alignments, using mapping rules to extract the biology of interest (e.g. ribosomal P-sites, et c) from the alignments.
Output files¶
Tracks can be output in wiggle and bedGraph formats. Because these formats are unstranded, two files are created:
- OUTBASE_fw.wig
Counts at each position for the plus/forward strand of each chromosome
- OUTBASE_rc.wig
Counts at each position for the minus/reverse strand of each chromosome
where OUTBASE is given by the user.
See also¶
- Read mapping functions
Explanations of mapping rules and why they can be useful
plastid.genomics.map_factories
For lists of mapping rules and their parameters
- plastid.bin.make_wiggle.main(argv=['-T', '-E', '-b', 'html', '-d', '_build/doctrees', '-D', 'language=en', '.', '_build/html'])[source]¶
Command-line program
- Parameters
- argvlist, optional
A list of command-line arguments, which will be processed as if the script were called from the command line if
main()
is called directly.Default: sys.argv[1:] (actually command-line arguments)