Quanyu Chen
The lateast version of `pysam` is `v0.22.1` and yours is `v0.22.0`. However, I found the attribute `is_mapped` in the document of `v0.22.0`. So maybe I should check your enviroment... And...
I have tried your enviroment and ran GCI with my tested data, and finally it run properly. And I have found in my another enviroment with an older version of...
Oh actually, there are some problems of dependency conflicts in your enviroment: there is no matplotlib! And when installed matplotlib I got ``` (gci_issue) [chenquanyu@login2 MH63]$ pip install matplotlib Looking...
I'm sorry for not giving the test file due to the large size. You can just download sequencing reads of CHM13v2.0 and align reads to the assembly. Be cautious, you...
Sorry for delaying reply. Now you can test GCI on the downsampled files from [zenodo](https://zenodo.org/records/12748594). Please look at the latest README.
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...
I will close this issue due to long time of inactivity.
Now, in the latest beta version (commit `9a15e91`), you can get a summarized GCI score in the file named `${prefix}.regions.gci` if providing regions file with `-R`
I will close this issue due to long time of inactivity.
Because GCI was designed for high-quality genome assembly, so you need to input whole genome alignment which means all chromosomes will be plotted. If not, the other chromosomes would be...