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Transipedia / dekupl-run

Identify differentially expressed k-mers between RNA-Seq datasets
MIT License
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inconsistency between documentation & snakemake file #58

Closed leclercfl closed 5 years ago

leclercfl commented 5 years ago

it seems there is an inconsistency between the documentation and what's in the snakefile for the statistical tests at the gene level; the choice of test is ambiguous if the gene_diff_method is not specified in the configuration file.

in the documentation: gene_diff_method: Method used for gene differential testing (default: 'DESeq2' or 'limma-voom' if number of samples > 100). Possible choices are 'DESeq2' and 'limma-voom'. 'limma-voom' is a faster alternative for large cohorts.

in the snakemake file (lines 169-174): AUTOMATICALLY SET GENE DIFF METHOD TO LIMMA-VOOM IF MORE THAN 100 SAMPLES if 'gene_diff_method' not in config : if len(SAMPLE_NAMES) >= 100: GENE_DIFF_METH = "DESeq2" else: GENE_DIFF_METH = "limma-voom"

jaudoux commented 5 years ago

@leclercfl Thanks for pointing that out!

Can you make a Pull Request with an updated documentation, please ?

MarineAGLAVE commented 5 years ago

I submitted a correction by Pull Request. And it's been validated! So I close this issue.