Merge branch 'main' of https://github.com/MMARINeDNA/metabarcoding_QA…

…QC_pipeline merging report.
kimparsons · Aug 11, 2023 · 525722f · 525722f
2 parents 88a0b80 + 2d76293
commit 525722f
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diff --git a/bin/dada2QAQC.R b/bin/dada2QAQC.R
@@ -60,10 +60,10 @@ for (i in 1:nrow(primer.data)){
 
 ### Plot Quality Scores and Save ----------------------------------
     png(filename=file.path(output_location,"logs",paste0(run_name,"_",primer.data$locus_shorthand[i],"_forward.png")))
-    plotQualityProfile(fnFs[1:4])
+    plotQualityProfile(fnFs)
     dev.off()
     png(filename=file.path(output_location,"logs",paste0(run_name,"_",primer.data$locus_shorthand[i],"_reverse.png")))
-    plotQualityProfile(fnRs[1:4])
+    plotQualityProfile(fnRs)
     dev.off()
 
 ### Find quality trimming length ----------------------------------
@@ -99,7 +99,7 @@ for (i in 1:nrow(primer.data)){
      }
      where_trim_all_Rs <- median(trimsR)
 
-    # for shorter sequences, check if the trim is too long
+    # Trim to max_trim value if the obtaided length is greater that max_trim
     if(where_trim_all_Fs > primer.data$max_trim[i]){
       where_trim_all_Fs <- primer.data$max_trim[i]
     }