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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
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Attempting to use QTLseqR..learning :) #20

Closed ShakerKousik closed 5 years ago

ShakerKousik commented 5 years ago

Hi Ben I just downloaded QTLseqr latest version and tried to run the example. It kept giving the below message. Thanks for any help. Shaker

df<-importFromGATK(file = file, highBulk = HighBulk, lowBulk = LowBulk, chromList = Chroms) Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file 'SNPs_from_GATK.table': No such file or directory

floschill commented 5 years ago

Hi Shaker, you probably tried executing the following code:

#load the package
library("QTLseqr")

#Set sample and file names
HighBulk <- "SRR834931"
LowBulk <- "SRR834927"
file <- "SNPs_from_GATK.table"

#Choose which chromosomes will be included in the analysis (i.e. exclude smaller contigs)
Chroms <- paste0(rep("Chr", 12), 1:12)

#Import SNP data from file
df <-
    importFromGATK(
        file = file,
        highBulk = HighBulk,
        lowBulk = LowBulk,
        chromList = Chroms
     )

This requires a table-file called "SNPs_from_GATK.table" in your working directory, which is not provided by QTLseqr when you just download and install the package. I would recommend reading the vignette (here), starting with the chapter "Standard workflow", that also describes how to download and use the Yang2013 example data. Flo

bmansfeld commented 5 years ago

closed