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yeeus / GCI

A program for assessing the T2T genome continuity
MIT License
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some questions about input file #6

Closed Hanjunmin closed 3 weeks ago

Hanjunmin commented 6 months ago

Hi, It's a great tool! but i don't know how to input my depth file when used the plot_depth.py,can you give me an example? I also suggest that you cam add some unusual input sample files on github. Thank you

yeeus commented 6 months ago

The depth file provided for plot_depth.py is generated by GCI which is in a fasta-like format (and gzipped):

>chromosome_id
0
1
2
3
...

And if you only need to use plot_depth.py with your customed depth file (such as the outputs from samtools depth), you can convert that into this format. And I will provide a script for that later (you would see it in the directory utility). Could you show me the format of your depth file?

yeeus commented 3 weeks ago

I will close this issue due to long time of inactivity.