trying to change length of barcode
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@luciacaceres-10601
Last seen 7.9 years ago

HI,

When I type the following in edgeR:

> # Process raw sequences from fastq file
> x = processAmplicons("Index2.Plate_10.fastqsanger", barcodefile="Samples1.txt",
+     hairpinfile="Hairpins1-10.txt", hairpinStart=28, hairpinEnd=50, verbose=TRUE)

I get the following error:
Error in processAmplicons("Index2.Plate_10.fastqsanger", barcodefile = "Samples1.txt",  :
  Barcode sequence length is set to 5, there are barcode sequence not with specified length.

It is true my barcode length is 6 not 5. How can I change this on edgeR? I can't seem to find the script that I can edit anywhere on the edgeR program/folder.

 

Thanks

processamplicons edger barcode • 1.1k views
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@mattritchieau-10604
Last seen 7.9 years ago

Try changing the barcodeEnd argument (maybe set this to 6 in your case if they are 6 bases long and start at position 1 in each read), or if need be both barcodeStart and barcodeEnd to suit the length and position of the sample indexes in your sequence reads. They need to be in a fixed position for processAmplicons to work for you though.

 

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@luciacaceres-10601
Last seen 7.9 years ago

Thank you. I was able to change it in R. I typed:

> fix(processAmplicons)

and a window popped up where I could make edit to the script.

 

Thanks,

Lucia

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Are you sure you need to use fix? Both barcodeStart and barcodeEnd are arguments to processAmplicons and can be changed in the function call, there's no need to modify the body of the function.

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@luciacaceres-10601
Last seen 7.9 years ago

I am so new to R that to be honest I don't know, I'll I can say is that I am not getting the problem anymore. However, this is not a permanent change because as soon as I closed the program it reverts any changes that I made to the script changes to the original format, which I can live with that.

How do you get to the function call? sorry about this silly question but I just have no background in bioinformatics.

thanks,

Lucia

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  1. Use the "Add comment" button to respond to posts.
  2. Look at ?processAmplicons for arguments that can be changed in the function call.
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