Errors in Step 15 - Githubissues

broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq

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Errors in Step 15 #460

Open parkjooyoung99 opened 2 years ago

parkjooyoung99 commented 2 years ago

Hello, I am using infercnv with my data and some samples are having 2 types of errors in step 15.

and below is my code

infercnv::run(b, cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics out_dir='./', cluster_by_groups=T, denoise=TRUE, HMM=FALSE, save_rds = F, plot_steps = F ,save_final_rds = F ,output_format = 'pdf')

Can anybody help where that errors occur?

Thank you!

GeorgescuC commented 2 years ago

Hi @parkjooyoung99 ,

I added a fallback to the simpler Leiden clustering method for chromosomes that have too few genes in the latest commit, so updating from the master branch should solve the issue you are encountering.

Regards, Christophe.