The output file "infercnv.observations.txt " not produced

broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq

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The output file "infercnv.observations.txt " not produced #554

Open imrjesh opened 1 year ago

imrjesh commented 1 year ago

Hi All I am using the infercnv_1.15.3 version of inferCNV package. When i go through the type of output file infercnv, does produces as an output as shown in link - https://github.com/broadinstitute/inferCNV/wiki/Output-Files One of the file named "infercnv.observations.txt" doesnt appear in output directory. This will be needed for further CNV score estimation within each cluster. Can you help me in getting this file?

phoebee-h commented 1 year ago

Hello, I am just the user. Happened to see a similar issue as yours. Maybe there is a parameter "write_expr_matrix=TRUE" that can be set as described in https://github.com/broadinstitute/infercnv/issues/481?

GeorgescuC commented 1 year ago

Hi @imrjesh ,

As @phoebee-h said, using the write_expr_matrix=TRUE option in either run() or plot_cnv() will make it so that output is generated again.

Regards, Christophe.