search

gtonkinhill / panaroo

An updated pipeline for pangenome investigation
MIT License
265 stars 33 forks source link

Question #111

Closed smb20200615 closed 3 years ago

smb20200615 commented 3 years ago

Hello,

Thank you for your wonderful tool. I have three questions. 1) I often get output such as group_2686 in the gene_presence matrix. Where can I find the genomes that contributed to this gene cluster? 2) Also, I am interested in annotating the genes reported in the gene-presence absence matrix. Where can I get the associated gene sequence for example for group_2686 to be used annotation via eggnog? 3) Finally, I was wondering if there is a way to make a manhattan plot from the output from panaroo + pyseer. I can't find the location of such genes in the genome (GFF file?). Is that reported somewhere in panaroo?

Many thanks!

gtonkinhill commented 3 years ago

Hi,

  1. The genes for each cluster are given in the gene_presence_absence.csv file.
  2. The gene names given in this file can be associated with the sequence and annotations by looking for their entry in the gene_data.csv file.
  3. I'm afraid not. This is a pretty tricky problem we are currently working on. As the genes are located in a graph rather than a single reference, it is not straightforward to work out what a sensible distance is between two genes. Taking the shortest path in the graph tends to give pretty poor results as mobile genetic elements can cause issues leading to very short distance estimates.

Hopefully this helps!

cizydorczyk commented 3 years ago

Thanks for the update. I deleted my post as I figured it out after re-reading the documentation carefully. The pan_genome_reference.fa file is exactly what I needed.

Thanks!

On Thu, Jun 3, 2021 at 3:39 PM Gerry Tonkin-Hill @.***> wrote:

Closed #111 https://github.com/gtonkinhill/panaroo/issues/111.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/gtonkinhill/panaroo/issues/111#event-4839913567, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFONJDBYW3G33URVLGJG3RDTQ7Y73ANCNFSM43L77OEA .