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yeeus / GCI

A program for assessing the T2T genome continuity
MIT License
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only for one chromosome #3

Open JhinAir opened 6 months ago

JhinAir commented 6 months ago

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

C021-CHA-S01_2-01_ont chrY_RagTag

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

Thanks

yeeus commented 6 months ago

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 considered as assembled so poorly that having no highly-confident alignments. And I added the option -R to plot specific regions in the new version v0.2, so you can input one bed file to specifically plot some regions.

yeeus commented 4 months ago

Some others have also inquired about this issue, so I decide to add one option instead of iterating through all headers. I now reopen this issue until it would be fixed.

yeeus commented 4 months ago

Now GCI adds one option --chrs to specify chromosomes (in commit 7afb709)