I am still learning to use STAR and could not pass this error after googling the errors
STAR --runThreadN 8 \ --runMode alignReads \ --genomeDir /home/groups/user/genomeDir \ --readFilesIn /home/groups/user/bulk_RNA-seq/sample1/sample1_1.fq \ --outSAMtype BAM Unsorted EXITING because of fatal input ERROR: could not open readFilesIn=Read1
Would you please tell what I miss here? For pair end read, path to read 2 will following read 1 with a space or a comma? I appreciate your help!
Update: I could read the fastq file now but still not sure about the input for the pair end read.