mnshgl0110
commented
3 years ago Hello,
Plotsr can use a bed file to have additional annotation in the plot. But this is still work in development and is not finalised yet.
You can get a plot like this:
By parsing a BED file with this data:
Chr1 10000000 10000001 R . red 12
Chr2 5000000 5000001 Q ^ black 6 black marker black 6
Chr3 12000000 12000010 R , #78AB46 12 The columns of the BED file are:
Chromosome ID
0-based start coordinate
1-based end coordinate
Genome to annotatte (R/Q)
Marker (Similar to defined here: https://matplotlib.org/stable/api/markers_api.html)
Marker colour (Named color acceptable to matplotlib https://matplotlib.org/stable/gallery/color/named_colors.html or in hexadecimal)
Marker size
Annotations text (Optional)
Annotations text color (Optional, Named color acceptable to matplotlib https://matplotlib.org/stable/gallery/color/named_colors.html or in hexadecimal)
Annotations text size (Optional)You can use it but please note that the BED file structure would change in future.
JiaoLaboratory
Hello，Nice work for SYRI ! I am using syri to detecte Structural variations and using plotsr for plotting, But always meeting error" plotsr syri.out $refgenome $qrygenome -o png -B bed
Incomplete data in BED file line: 'contig41', '129765', '141675', 'utg41', '58816', '70726', 'SYN', '1505', '1505' Marker information (type, col, size) is necessary. Text annotation (text, col, size) is optional"
I don't know what is the error of my bed file. Could you please give me a exmple bed format? Thank You very ! @wen-biao @mnshgl0110 @HeQSun