additional fix issue with large pacbio library dereplication; this is…

… rare so we may want to make this a setable option
h3abionet · Feb 8, 2024 · 90cdee8 · 90cdee8
1 parent ecdf2f6
commit 90cdee8
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/templates/DadaPooled.R b/templates/DadaPooled.R
@@ -21,7 +21,9 @@ if(pool != "pseudo"){
   pool <- as.logical(pool)
 }
 
+dereps <- derepFastq(filts, n=100000, verbose=TRUE)
+
 cat(paste0("Denoising ${readmode} reads: pool:", pool, "\\n"))
-dds <- dada(filts, err=err, multithread=${task.cpus}, pool=pool)
+dds <- dada(dereps, err=err, multithread=${task.cpus}, pool=pool)
 
 saveRDS(dds, "all.dd.${readmode}.RDS")