config.yaml changed and how to rerun

[hermean]

Dear developers,

I have a question about config.yaml change - after i finished one successful run of AE and AS, I would like to change the fpkm cutoff of AE (from 1 to 0.5) and rerun the pipeline. As I maintained all the other information unchanged (including root folder and sample annotation files), i found "snakemake aberrantExpression" did 0 job. How do I rerun this with fpkm cutoff change, but without the need to recalculate everything else (as i have over 200 samples, and it takes a long time to re-do everything)?

Thanks very much!

Hermean

[vyepez88]

Hi Hermean,
I added a Discussion that might help: #590
In your case, the fpkm affects the filtering, so you would need to indicate the ods_unfitted.Rds as the output file (please provide the full path). See this script: https://github.com/gagneurlab/drop/blob/master/drop/modules/aberrant-expression-pipeline/Counting/filterCounts.R