You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I have {graph_name}.full.gbz files generated from Cactus Minigraph to map short-read data. According to the tutorial, a filtered graph is more efficient for vg giraffe. Additionally, I noticed that Haplotype Sampling is a better option for vg giraffe, requiring a clipped .gbz graph and a .hapl file.
How can I generate the filtered/clipped version of the graph and haplotypes without having access to the original input files?
I tried the following steps but am not sure if they are correct: (I only have full.hal full.gbz. full.gfa files)
vg convert -g <(gunzip -c {graph_name}.full.gfa.gz) > {graph_name}.full.vg
cactus-graphmap-join --vg {graph_name}.full.vg --hal {graph_name}.full.hal --giraffe clip ...
Any suggestions or corrections to this approach would be greatly appreciated. :)
The text was updated successfully, but these errors were encountered:
EEEdyeah
changed the title
How to manually generate a Clipped/Filtered Graph from a {graph_name}.full.gbz File produced by the MC pipeline?
Generating a Clipped/Filtered Graph from a {graph_name}.full.gbz File produced by the MC pipeline?
Nov 23, 2024
Hello,
I have {graph_name}.full.gbz files generated from Cactus Minigraph to map short-read data. According to the tutorial, a filtered graph is more efficient for vg giraffe. Additionally, I noticed that Haplotype Sampling is a better option for vg giraffe, requiring a clipped .gbz graph and a .hapl file.
How can I generate the filtered/clipped version of the graph and haplotypes without having access to the original input files?
I tried the following steps but am not sure if they are correct: (I only have full.hal full.gbz. full.gfa files)
vg convert -g <(gunzip -c {graph_name}.full.gfa.gz) > {graph_name}.full.vg
cactus-graphmap-join --vg {graph_name}.full.vg --hal {graph_name}.full.hal --giraffe clip ...
Any suggestions or corrections to this approach would be greatly appreciated. :)
The text was updated successfully, but these errors were encountered: