"Error: unexpected '=' in processAmplicon in edgeR

[Roberta_Chiavetta]

Hi everyone,

I have a problem with edgeR. I need to use the processAmplicon function and I'm copying the following code:

> library(edgeR)
> sampleanno <- read.table("Samples4.txt", header=TRUE, sep="\t")
> sgseqs <- read.table("sgRNAs4.txt", header=TRUE, sep="\t")
> x <- processAmplicons("screen4_R1.fastq", readfile2="screen4_R2.fastq",
+ barcodefile="Samples4.txt", hairpinfile="sgRNAs4.txt",
+ verbose=TRUE)

from the edgeR using guide. Of course, I'm substituting the correct file names to the ones provided as examples in the guide.

The problem is that the error:

"Error: unexpected '=' in:
"x <- processAmplicons("C:/Users/chiav/Desktop/RUN_230601/Barbieri_A_S15_R1_001.fastq/A_R1_001.fastq",
+ barcodefile=" 

keeps appearing and I don't understand where the problem is. I also tried to shorten the file names in order to make everything appear on one line, to preserve the correct format, but nothing changes.

Do someone of you ever had the same problem? Can someone help me?

Thanks everyone!

[nirgrahamuk]

My best guess is that you are naively copying/modifying R code that you found in the console, or that was represented as coming from the console, such that there are + signs there indicating a continuation of code; where this is in fact invalid R code and will mess with the interpretation of your code

 > x <- processAmplicons("screen4_R1.fastq", readfile2="screen4_R2.fastq",
+ barcodefile="Samples4.txt", hairpinfile="sgRNAs4.txt",
+ verbose=TRUE)

The above is not runnable code in principle.

 x <- processAmplicons("screen4_R1.fastq", readfile2="screen4_R2.fastq",
 barcodefile="Samples4.txt", hairpinfile="sgRNAs4.txt",
 verbose=TRUE)

This may be

[Roberta_Chiavetta]

Hi,

you are right, this seemed to be the problem. Now other errors appear, but that one seems solved.

Thank you!