Comments (3)
- Yeah, in the newest version of GCI (v0.4), I added the function to generate GCI scores for each specific region.
- As GCI is a tool for assesing genome continuity while plotting is just an additional function, GCI would plot all chromosomes in defaut. However, in the latest version, the script plot_depth.py in the directory
utility
can generate plots only for the sepcific regions if providing-R
option (as descripted in #4) - I'm so sorry for that,
out of memory
also happens to me usually. I do think I need to solve this problem some day. And good suggestions, I have added the funcion of logging in the latest version of GCI (v0.4), I wish that would help you...
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Thanks for quick reply and update!
Could you please provide a separate script for GCI score calculation of specific region like the plot script in the utility? Then I have not to run the whole process again since I got the depth.gz already~
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Yeah that's a good suggestion. Now in the latest commit, I created a file named GCI_score.py
in the folder utility
, which can be used to compute GCI score as in GCI.py and all you need is to provide the depth.gz file you got.
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Related Issues (10)
- can you make the depth plot a stand-alone function? HOT 2
- Why not use illumina reads? HOT 1
- only for one chromosome HOT 3
- Uniform window size for visualization HOT 3
- some questions about input file HOT 1
- a summarized GCI score for multiple specific regions HOT 1
- dealing with pacbiohifi HOT 12
- Curated contigs number can be zero ,even less than 1 HOT 1
- Killed the command HOT 1
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