I'm trying to use clinker with gff files. I want to use it to visualize genes from a same pangene. I think I got it to work on 2 genes, but it plotted the whole chromosomes (a long infinite line), which are 230Mb each, and hence it's basically impossible to view my genes.
What would you advise doing? Do I need to have a fasta of only my genes, and hence change all the coordinates from the gff?
EDIT:
I used bedtools getfasta to get only the fasta sequences of my 2 genes, and changed the coordinates in the gff so that the start will be 1 to match my new fasta. After running clinker it says it doesn't find CDS features.
See my files attached.
EDIT2: I didn't see the range option, now I can visualize the genes. I'll close my issue.
Ultimately I'm trying to use it to visualize exons similarity rather than the whole genes.
Hello,
I'm trying to use clinker with gff files. I want to use it to visualize genes from a same pangene. I think I got it to work on 2 genes, but it plotted the whole chromosomes (a long infinite line), which are 230Mb each, and hence it's basically impossible to view my genes.
What would you advise doing? Do I need to have a fasta of only my genes, and hence change all the coordinates from the gff?
EDIT: I used bedtools getfasta to get only the fasta sequences of my 2 genes, and changed the coordinates in the gff so that the start will be 1 to match my new fasta. After running clinker it says it doesn't find CDS features.
See my files attached.
EDIT2: I didn't see the range option, now I can visualize the genes. I'll close my issue.
Ultimately I'm trying to use it to visualize exons similarity rather than the whole genes.
Best, Julie
Zmays-B73-v5_chr_2.Zm00001eb078740.updatedcoord.fasta.txt Zmays-B73-v5_chr_2.Zm00001eb078740.updatedcoord.gff3.txt Zmays-B97_chr_2.Zm00018ab080830.updatedcoord.fasta.txt Zmays-B97_chr_2.Zm00018ab080830.updatedcoord.gff3.txt