search

madagiurgiu25 / decoil-pre

Reconstruct ecDNA from long-read data using Decoil tool
BSD 3-Clause "New" or "Revised" License
8 stars 0 forks source link

visualising the output of decoil #7

Closed eesiribloom closed 6 months ago

eesiribloom commented 8 months ago

If I have this output from decoil, which files can I use to visualise any potential ecDNA. The manuscript mentions using gGnome clean.vcf config.json coverage.bw fragments_clean_1.bed fragments_clean_2.bed fragments_clean_3.bed fragments_initial.bed graph.gpickle logs metrics_frag_cov_distribution.png metrics_frag_len_cov_correlation.png metrics_frag_len_distribution.png reconstruct.bed reconstruct.bed_debug reconstruct.ecDNA.bed reconstruct.json reconstruct.links.txt_debug sv.sniffles.bedpe sv.sniffles.vcf

madagiurgiu25 commented 6 months ago

Dear @eesiribloom,

I have created a separate repository for the visualization -> https://github.com/madagiurgiu25/decoil-viz

You would need the following files output by Decoil:

eesiribloom commented 6 months ago

Okay thanks, for some reason these were not produced except coverage.bw (as mentioned in this issue)

madagiurgiu25 commented 6 months ago

@eesiribloom, can I close this issue? Let me know if you have other questions. Best, Madalina