I have this RNA-seq fastq file which is SINGLE-end.
However, I couldn't figure out these fastq files are unstranded or strand-specific.
I cannot even know if their orientation is forward or reversed...
I ran STAR alignment with command:
STAR --runThreadN 32 --genomeDir [ENSEMBL reference folder] \ --readFilesIn [fastq file name] --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts \ --outFileNamePrefix [output file name]
but when I convert the result to cpm and compare it to paper's cpm matrix, it's quite different.
What should I do?