Hi All. I'm trying to an alignment for multiple files, paired end, using Rsubread. I set up the readfile vector with file names as follows.
read1 <- list.files(path= "path to/Yarrowia_lipolytica/Genewiz-us-ngs-00_fastq", pattern = "*_R1_001.fastq.gz$") read2 <- list.files(path= "path to/Genewiz-us-ngs-00_fastq", pattern = "*_R2_001.fastq.gz$")
That seems to work, in example reads1 appears to be chr [1:24] "F353-B-gku_R1_oo1.fasta.gz"....
But, when I try to run align, as follows, I get an error that is a mystery to me.
align(index = "index", readfile1 = reads1, readfile2 = reads2, output_file = "./Rsubread_alignment.BAM", input_format = "FASTQ", output_format = "BAM") Error in normalizePath(files, mustWork=mustWork) : path = "F353-B-gku_R1_oo1.fasta.gz".: No such file or directory
I wonder if the file names need the whole path attached somehow?
Any help would be much appreciated.