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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
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why there are two kinds of line in the tracks related to gene density? #83

Closed futurefanzhang closed 2 months ago

futurefanzhang commented 3 months ago

Hi, I want to ask why there are two kinds of lines Weixin Screenshot_20240802113844 Which one represents genes? To make the gene density clearer, can I display only one type of line?

mnshgl0110 commented 3 months ago

The mRNAs regions are shorter lines and the CDS regions are the longer lines. For example, see the annotation of a gene below:

Chr1    TAIR10  gene    3631    5899    .       +       .       ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
Chr1    TAIR10  mRNA    3631    5899    .       +       .       ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
Chr1    TAIR10  protein 3760    5630    .       +       .       ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
Chr1    TAIR10  exon    3631    3913    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  five_prime_UTR  3631    3759    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     3760    3913    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    3996    4276    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     3996    4276    .       +       2       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    4486    4605    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     4486    4605    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    4706    5095    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     4706    5095    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    5174    5326    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     5174    5326    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    5439    5899    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     5439    5630    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  three_prime_UTR 5631    5899    .       +       .       Parent=AT1G01010.1

Which one represents genes? To make the gene density clearer, can I display only one type of line?

I think, you can filter the GFF to only have the mRNA regions. That should plot only one type of line.

futurefanzhang commented 2 months ago

Thank you. I generated the ideal figure only using mRNA regions