given that bamcov_cmd is used in the DNA-mapping / ATAC wf and genera…

…tes files named seq_depth_norm, RPKM is more appropriate
maxplanck-ie · Aug 9, 2024 · cada3ec · cada3ec
1 parent e1c79ba
commit cada3ec
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/snakePipes/shared/tools/deeptools_cmds.snakefile b/snakePipes/shared/tools/deeptools_cmds.snakefile
@@ -76,7 +76,7 @@ bamcov_cmd = """
                 -o {output} \
                 --binSize {params.bwBinSize} \
                 -p {threads} \
-                --normalizeUsing RPGC \
+                --normalizeUsing RPKM \
                 --effectiveGenomeSize {params.genome_size} \
                 {params.ignoreForNorm} \
                 {params.blacklist} \