Hello again, I'm working on the RnaSeqGeneEdgeRQL workflow at the moment, trying to edit it so that it uses my own data rather than importing published RNASeq data from SRA...
I was wondering if there is any easier way to do it.
The original instructions to create the vector were: (If I got it right, basically, I have to act so that my all.fastq object contains my own data rather than using SRA ones...)
##Just creating a targets file targetsFile <- system.file("extdata", "targets.txt", package="RnaSeqGeneEdgeRQL") targets <- read.delim(targetsFile, stringsAsFactors=FALSE) targets ##Retrieving data for (sra in targets$SRA) system(paste("fastq-dump", sra)) all.fastq <- paste0(targets$SRA, ".fastq") ##Here is the next original function which requires the all.fastq object all.bam <- sub(".fastq", ".bam", all.fastq) align(index="mm10", readfile1=all.fastq, input_format="FASTQ", output_file=all.bam)
I looked for a proper solution online, then I tried with the readFastq function from ShortRead package, as follows:
fastqPath <- list.files("/home/genomica/DATA/dwarf/fastq", pattern = ".fastq$", full = TRUE) reads <- readFastq(fastqPath)
all.bam <- sub(".fastq", ".bam", reads) align(index="FASTA", readfile1=reads, input_format="FASTQ", output_file=all.bam)
That's what I did, also visualizing the contents of the reads and fastqPath objects.
It looks as if I managed to create the desider object, but in the wrong format (belonging to the ShortRead class rather than the required vector). As a matter of fact, when trying to go further, I get the
No method for coercing this S4 class to a vector
How can I overcome this issue and use the pipeline with a proper vector object containing local data?
Here is my sessioninfo() output: