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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Problem retrieving infercnv.observations.txt and infercnv.references.txt output files #605

Closed RoyPollak closed 1 year ago

RoyPollak commented 1 year ago

Hey InferCNV team, thank you very much for making this bioinformatic tool easily and freely accessible! :)

After running the run() function, I didn't manage to find infercnv.observations.txt and infercnv.references.txt output files in the output directory.

This is the code I ran: run(male_only_infercnv_obj, out_dir = 'InferCNV_output', cutoff = 1, cluster_by_groups = TRUE, denoise = TRUE, HMM = FALSE, window_length = 101)

I will be very happy if you could instruct me how can I retrieve this file, or else, what am I doing wrong?

With many thanks. Roy

RoyPollak commented 1 year ago

Executing run(..., write_expr_matrix = TRUE) outputs infercnv.observations.txt and infercnv.references.txt files.