Comments (1)
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.
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Related Issues (13)
- Marker file reference HOT 1
- Empty fasta file. HOT 8
- I cannot run the example HOT 3
- Retrieve haplotype sequence HOT 1
- dna read reconstruction HOT 4
- Final Results HOT 6
- Errors running createFinalHaplotypTable function HOT 3
- a bug and a question HOT 2
- problem during installing Rswarm and Rvsearch HOT 9
- Issue installing haplotypeR HOT 3
- Running Example HOT 5
- Installation error for Rswarm and Rsearch on Windows 10, R version=4.1 HOT 1
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