sanger-pathogens
Add track with contig placements to Circos plots
It could be useful to a user to see what contigs map to a target pseudochromosome. It should be evaluated whether Circos allows to label such regions with contig IDs in a separate track.
Would you be able to provide the commands to do it or maybe even be able to modify the nf file?
I have experimented a little but but it's quite nontrivial to do if we also want all the labels for contigs in there. This will blow the image up immensely if there are many contigs. It might be possible to only enable this feature if the number of contigs is less than a reasonable threshold.
Regarding your question, this would be something that is quite closely tied to the Circos input generation, and difficult to do on the Companion end output (most of the intermediate data used to make the plots is not kept at this stage). However, you might be able to use the AGP files present in the Companion output to roll your own solution -- they describe the mappings completely.
@mictadlo BTW if you're the Michal Lorenc I know from the ZBH, then hi and long time no see!
Hi Sascha, Yes, its me. Congratulation to your job and thank you for your response.