I have TCGA Breast raw sequencing data fastq files. Initially with one of the sample bam file I used
Rseqc to check whether it is strand specific or not.
I see that it is Strand specific
RF (reverse forward strandness). I have aligned all the samples with
hisat2 using the argument
But now somewhere I saw that all the TCGA samples are Un-stranded.
Can anyone please tell whether the data is strand specific protocol or not?