maf

Description

A track for MAF (multiple alignment format). See the format description from UCSC.

Parameters

Necessary:

  • file

  • reference

Optional:

  • title: Put here a title which will apprear on the right.

  • height: 0.5 (default) or float above 0.

  • overlay_previous: no (default) or yes or share-y.

  • orientation: by default this option is not set but you can also put: inverted.

  • line_width: 0.5 (default) or any float above 0

  • file_index: by default this option is not set

  • color_identical: black (default)

  • color_mismatch: grey (default)

  • color_gap: lightgrey (default)

  • species_order: by default this option is not set

  • species_labels: by default this option is not set

  • species_order_only: false (default) or true.

  • display_ref_seq: false (default) or true.

Output of make_tracks_file:

# title of track (plotted on the right side)
title =
# height of track in cm (ignored if the track is overlay on top the previous track)
height = 2
# if you want to plot the track upside-down:
# orientation = inverted
# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
# Otherwise, each plot use its own scale
#overlay_previous = yes

# In addition to the maf file the reference genome is required:
# For example
#reference = mm10
# To speed the access to specific region
# The maf file needs an index.
# The default is the file
# followed by '.index'. Alternatively another
# file can be specified.
# If it does not exists it will be created:
#file_index =
# Set colors
#color_identical = black
#color_mismatch = grey
#color_gap = lightgrey
# Set line_width
#line_width = 0.5
# optional: the species order
#species_order = hg18 panTro2
# optional if species_order is specified (don't use space in names)
#species_labels = human chimpanzee
# optional if species_order is specified and they are the only one you want:
#species_order_only = true
# optional if you want to see the DNA sequence of the ref
#display_ref_seq = true
# optional: If not given is guessed from the file ending.
file_type = maf