Comment ankur Member #601 09/12/2018 at 10h17 Problem in converting the SRA file to fastq file Error- fastq-dump --split-3 SRR5873811 sh: 1: fastq-dump: not found fastq-dump --split-3 SRR5873810 sh: 1: fastq-dump: not found fastq-dump --split-3 SRR5873809 sh: 1: fastq-dump: not found fastq-dump --split-3 SRR5873808 sh: 1: fastq-dump: not found I had install the SRA tool kit using following command- > tar xzvf sratoolkit.2.9.2-ubuntu64.tar.gz and > export PATH=$PATH:/directory/sratoolkit.2.4.1-ubuntu64/bin Then, i had downloaded the SRA file in R platform using following command line- > sri<-read.csv("SraRunInfo.csv", stringsAsFactors=FALSE) > files<-basename(sri$download_path) > for(i in 1:length(files)) download.file(sri$download_path[i], files[i]) After that i tried to convert the SRA file to fastq file in R platform using following command- > for(f in files) { cmd = paste("fastq-dump --split-3", f) cat(cmd,"\n")#print the current command system(cmd) # invoke command } Awaiting for your kind reply. Best regard- Ankur Sahu, Tezpur University
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