Open canankolakoglu opened 1 year ago
Hi, can you verify that the gtf file used for the external counts is the same as for the local samples?
Hi again,
Sure, here the config.yaml
(https://github.com/gagneurlab/drop/files/11622243/config.yaml.txt)
and sample_annotation
(https://github.com/gagneurlab/drop/files/11622249/sample_annotation.tsv.txt)
files that are used to create external counts.
Hi @canankolakoglu , sorry for the late follow up. From your error, this does not seem to be related to the external counts, but rather the use or not-use of subsets of genes during FDR correction. To figure out what is going on, can you run the AberrantExpression_pipeline_OUTRIDER_pvalsOutrider_R
script interactively until this line and report what the value of subsets
is at this point? Given your config.yaml file with genesToTest: null
(i.e. not using such subsets), the value should be NULL
Hi, I'm using drop 1.3.3 in order to do aberrant expression analysis. However during outrider execution with 2 bam data and 9 external counts, I'm getting the following error:
Here my
config.yaml
(https://github.com/gagneurlab/drop/files/11622184/config.yaml.txt) file andsample_annotation
(https://github.com/gagneurlab/drop/files/11622187/sample_annotation.tsv.txt) table Also you can find2023-05-30T144827.863094.snakemake.log
(https://github.com/gagneurlab/drop/files/11622192/2023-05-30T144827.863094.snakemake.log.txt) fileThanks.