Macintosh; Intel Mac OS X 10_10_5
Rstudio Version 0.99.903
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
I tried to use the 'Rsubread' package for doing an alignment between my RNAseq data and the index of the genome I just created and I have an error message (see below). I first thought that there was something wrong with the index I created but it seems that the error is most likely caused by the reading of the files. I double-checked and the names of the files are exactly identical to the names in the table and are located in the appropriate folder and I also tried to change the name of the FASTQ documents both in the .fastq and in the .txt but this didn't help. Could somebody help me to figure out what can be the cause of this problem and how to solve it? I thank you in advance.
> targets=read.delim("run_info2.txt",header=T) > targets FileName CellType Status Type 1 P4355_125_TCTCGCGC-TATAGCCT_L001_R1_001.fastq PM DMSO Ctrl 2 P4355_126_TCTCGCGC-ATAGAGGC_L001_R1_001.fastq PM AZD Down 3 P4355_127_TCTCGCGC-CCTATCCT_L001_R1_001.fastq White DMSO Ctrl 4 P4355_128_TCTCGCGC-GGCTCTGA_L001_R1_001.fastq White AZD Down 5 P4355_129_GAATTCGT-AGGCGAAG_L001_R1_001.fastq White EtOH Ctrl 6 P4355_130_CTGAAGCT-AGGCGAAG_L001_R1_001.fastq White Estr Ctrl 7 P4355_131_TAATGCGC-AGGCGAAG_L001_R1_001.fastq TOROE EtOH Ctrl 8 P4355_132_CGGCTATG-AGGCGAAG_L001_R1_001.fastq TOROE Estr Up > output.files=sub('.fastq','.bam',targets$FileName) > align('mm10',readfile1=targets$FileName,phredOffset=33,input_format='FASTQ',output_file = output.files) Error in file.exists(readfile1) : invalid 'file' argument