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Question: Error in processAmplicons "hairpin sequence length not with specified length"
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gravatar for lucia.caceres
18 months ago by
lucia.caceres0 wrote:

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,

 

ADD COMMENTlink modified 18 months ago by Matthew Ritchie660 • written 18 months ago by lucia.caceres0
0
gravatar for Matthew Ritchie
18 months ago by
Australia
Matthew Ritchie660 wrote:

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,]
ADD COMMENTlink written 18 months ago by Matthew Ritchie660

Thank you for the code. It helped a lot.

ADD REPLYlink written 18 months ago by lucia.caceres0
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