table of contents
| LAST-DOTPLOT(1) | User Commands | LAST-DOTPLOT(1) |
NAME¶
last-dotplot - make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format
SYNOPSIS¶
last-dotplot --help
last-dotplot [options] maf-or-tab-alignments dotplot.png
last-dotplot [options] maf-or-tab-alignments dotplot.gif
...
DESCRIPTION¶
Draw a dotplot of pair-wise sequence alignments in MAF or tabular format.
OPTIONS¶
- -h, --help
- show this help message and exit
- -v, --verbose
- show progress messages & data about the plot
- -x INT, --width=INT
- maximum width in pixels (default: 1000)
- -y INT, --height=INT
- maximum height in pixels (default: 1000)
- -m M, --maxseqs=M
- maximum number of horizontal or vertical sequences (default=100)
- -1 PATTERN, --seq1=PATTERN
- which sequences to show from the 1st genome
- -2 PATTERN, --seq2=PATTERN
- which sequences to show from the 2nd genome
- -c COLOR, --forwardcolor=COLOR
- color for forward alignments (default: red)
- -r COLOR, --reversecolor=COLOR
- color for reverse alignments (default: blue)
- --alignments=FILE
- secondary alignments
- --sort1=N
- genome1 sequence order: 0=input order, 1=name order, 2=length order, 3=alignment order (default=1)
- --sort2=N
- genome2 sequence order: 0=input order, 1=name order, 2=length order, 3=alignment order (default=1)
- --strands1=N
- genome1 sequence orientation: 0=forward orientation, 1=alignment orientation (default=0)
- --strands2=N
- genome2 sequence orientation: 0=forward orientation, 1=alignment orientation (default=0)
- --max-gap1=FRAC
- maximum unaligned (end,mid) gap in genome1: fraction of aligned length (default=0.5,2)
- --max-gap2=FRAC
- maximum unaligned (end,mid) gap in genome2: fraction of aligned length (default=0.5,2)
- --pad=FRAC
- pad length when cutting unaligned gaps: fraction of aligned length (default=0.04)
- -j N, --join=N
- join: 0=nothing, 1=alignments adjacent in genome1, 2=alignments adjacent in genome2 (default=0)
- --border-pixels=INT
- number of pixels between sequences (default=1)
- --border-color=COLOR
- color for pixels between sequences (default=black)
- --margin-color=COLOR
- margin color
- Text options:
- -f FILE, --fontfile=FILE
- TrueType or OpenType font file
- -s SIZE, --fontsize=SIZE
- TrueType or OpenType font size (default: 14)
- --labels1=N
- genome1 labels: 0=name, 1=name:length, 2=name:start:length, 3=name:start-end (default=0)
- --labels2=N
- genome2 labels: 0=name, 1=name:length, 2=name:start:length, 3=name:start-end (default=0)
- --rot1=ROT
- text rotation for the 1st genome (default=h)
- --rot2=ROT
- text rotation for the 2nd genome (default=v)
- Annotation options:
- --bed1=FILE
- read genome1 annotations from BED file
- --bed2=FILE
- read genome2 annotations from BED file
- --rmsk1=FILE
- read genome1 repeats from RepeatMasker .out or rmsk.txt file
- --rmsk2=FILE
- read genome2 repeats from RepeatMasker .out or rmsk.txt file
- Gene options:
- --genePred1=FILE
- read genome1 genes from genePred file
- --genePred2=FILE
- read genome2 genes from genePred file
- --exon-color=COLOR
- color for exons (default=PaleGreen)
- --cds-color=COLOR
- color for protein-coding regions (default=LimeGreen)
- Unsequenced gap options:
- --gap1=FILE
- read genome1 unsequenced gaps from agp or gap file
- --gap2=FILE
- read genome2 unsequenced gaps from agp or gap file
- --bridged-color=COLOR
- color for bridged gaps (default: yellow)
- --unbridged-color=COLOR
- color for unbridged gaps (default: orange)
| March 2021 | last-dotplot 1179 |