yeeus / gci Goto Github PK

Cool tool! I’m interested in specific regions, but I’m running into some issues with GCI.

1. Is it possible to generate a continuity index for a specific region?
2. When I plot the depth of a specific region, it also generates whole genome figures, which takes a long time. It doesn’t seem necessary, though.
3. It’d be awesome to add some logging since the tool needs a lot of memory. I keep hitting an ‘out of memory’ error in the first few runs, but I can’t check if the depth file has been generated. If you’ve got a log file, could you please check the last log entry so I can keep the GCI running?

Hi,
when I extract only one chromosome of bam and fasta files to run, GCI stills outputs all chromosomes. The other chromosomes are null but the desired chromosome also failed.

python /share/home/zhanglab/user/chenquanyu/scripts/GCI/GCI.py -r C022-CHA-S02_2-01.chrY.fa --nano C022-CHA-S02_2-01.chrY.bam -o C022-CHA-S02_2-01_ont -it png -p -ts 5 --force && touch C022-CHA-S02_2-01_ont.GCI.finish

Could you please add a parameter for specifically outputing one chromosome or one region?

Thanks

Useful tool,
I have a question: why not use the common illumina reads, could you add this function?

thanks！

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

hi developers,

I noticed in a case, the overall picture looks different from a zoom-in picture of a specific region. I guess this is because you use an adopted window size for different plots with different scales. Making it uniform will be better to compare each other.

Nice tool!

If I didn't add "-p" to generate the depth plot at first, I have to run it again, which is much more time-consuming. Could you make it a stand-alone function?