Updated how transcripts are pooled.

call-transcripts-timecourse.R

@@ -74,8 +74,8 @@ for (i in seq(1:length(args$experiment))){
     a2 = args$replicate2[i]
     alignments_1 = as(readGAlignments(a1), "GRanges")
     alignments_2 = as(readGAlignments(a2), "GRanges")
-    combined.replicates <- sort(c(alignments_1, alignments_2))
-    alignments <- sort(c(alignments,combined.replicates ))
+    combined.replicates <- sort(c(alignments_1, alignments_2,alignments))
+    alignments <- combined.replicates
 }