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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Can't find all branches' annotation for Clonality trees #471

Open doou0 opened 2 years ago

doou0 commented 2 years ago

17_HMM_predHMMi6.rand_trees.hmm_mode-subclusters.cell_groupings contains the results of CNV classification, one column in this file is the category names (1.1.1.1, 1.1.1.2, 1.1.2.1, 1.1.2.2, 1.2.1.1, 1.2.1.2, 1.2.2.1, 1.2.2.2)

my file included these catagories 1.1.1.1 | 23 1.1.1.2 | 16 1.1.2.1 | 12 1.1.2.2 | 15 1.2.1.1 | 21 1.2.1.2 | 6

Annotation of branches is in two files named "HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_regions.dat" and "HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_genes.dat" .

The question is "why the chromosome and state information of 1.2.1.1 ,1.2.1.2 are not included in these two files?("HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_regions.dat" and "HMM_CNV_predictions.HMMi6.rand_trees.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_genes.dat" )"

Thanks for any kind of help!!!

GeorgescuC commented 2 years ago

Hi @doou0 ,

These files only list predicted CNV regions and genes part of them, so in all likelihood, the 2 subclusters you are not seeing in those files have no identified CNVs. You can check the matching heatmap to see if such subclusters are indeed present.

Regards, Christophe.