Open APepey opened 2 years ago
Thanks for the information. First, I can not give you support for the code you got from WEHI (code using %>%), but I can help you with the merging reads. The code from WEHI combines multiple step into one step and makes it very difficult understand. It is far better to split up the code if you have issues. So just try to run the following lines individually and also read my instructions to Run HaplotypR on https://github.com/lerch-a/HaplotypR.
procReadsMerge <- mergeAmpliconReads(fastqFileR1 = as.character(marker_deplex$FileR1), fastqFileR2 = as.character(marker_deplex$FileR2), outputDir = 'merge_reads')
merged_reads <- cbind(marker_deplex[,c("SampleID", "SampleName","BarcodePair", "MarkerID")], procReadsMerge)
Make sure that the folder 'merge_reads' exists in getwd() !
If you still have issues, then please let me know.
Hello! Thank you for all your work! I have a question about one the HaplotypR functions.
I am working on MiSeq data with the HaplotypR package. I have 35 samples with five P. falciparum markers: ama1-d3, cpmp, csp, cpp and msp7. I could proceed with the following steps using an R code I received from the WEHI in December 2019:
I am then trying to merge paired ends but I am encountering different issues depending on the syntax I am trying:
Syntax 1:
Syntax 2:
Syntax 3:
Syntax 4:
What could I try to merge paired ends? Any help is appreciated, thank you. My
marker_table
is available here: https://gist.github.com/APepey/054e40b9a10f4b25987dc73b3421e2f5Here is my session info:
Thank you again!