Error in gen_final_features.R

[aussteiger1441]

Hi! Thank you for developing scE2G!

I encountered a error while running the pipeline snakemake -j1 --use-conda --configfile config/config.yaml with default config.yaml where the gen_final_features.R fails.

The error message is:

and here is the tail of log file:

I've also checked the input files (ActivityOnly_plus_external_features.tsv.gz, feature_table.tsv) and found that the column isSelfGenic is missing.

How could I resolve this issue? Thanks for your help!🥰

[mayasheth]

Hi, sorry you encountered this error! For a quick fix, you can edit the ENCODE_rE2G/workflow/scripts/feature_tables/gen_final_features.R script and remove isSelfGenic from the core_cols variable. It is simply an annotation of element-gene pairs indicating whether the element overlaps the gene body (introns or exons) of the target gene, and is not used as a feature for scE2G.

However, the column should be present and pulled through from the Predictions/EnhancerPredictionsAllPutative.tsv.gz file... if it is not in that file, the ABC submodule may not be up to date?