Hi,

When I type the following code:

> x = processAmplicons("Index2.Plate10.fastq", barcodefile="Samples1.txt",
+     hairpinfile="Hairpins sense.txt", hairpinStart=29, hairpinEnd=50, verbose=TRUE)
I get:

Error in processAmplicons("Index2.Plate10.fastq", barcodefile = "Samples1.txt",  :
  Hairpin sequence length is set to 22, there are hairpin sequences not with specified length.

I checked the length of my hairpin sequences, in my hairpin file/reference library and they are all 22nt long.

I don't understand what is going wrong. If you have any ideas of what I can do/check please let me know.

Thank,

This error message suggests you have hairpins of different lengths in your library.

To check if this is the case, try running something like: 

hp = read.delim("Hairpins sense.txt", stringsAsFactors=FALSE)
dim(hp)
summary(sapply(hp$Seq, FUN="nchar"))
which(sapply(hp$Seq, FUN="nchar")!=22)
hp[sapply(hp$Seq, FUN="nchar")!=22,]