Does anybody know how to fix the following error? When I type the following code:

# Process raw sequences from fastq file
x = processAmplicons("Index2.Plate10.fastq", barcodefile="Samples1.txt",
    hairpinfile="Hairpins1-10 - antisense.txt", hairpinStart=29, hairpinEnd=50, verbose=TRUE)

I get the following error:

Error in processAmplicons("Index2.Plate10.fastq", barcodefile = "Samples1.txt",  :
There are duplicate hairpin sequences.

I am kind of at a loss here. I don't know what to fix.

Thanks,

Lucia

Well, as the error message suggests, there are duplicate hairpin sequences in your hairpinfile. These sequences need to be unique, otherwise you wouldn't be able to correctly assign an amplicon to a single (targeted) gene.

Thanks, I thought the same thing but because I got this hairpin file, as an excel, from the company that sold us the entire library to run the screen, I wanted to make sure that I wasn't missing something.

Lucia