I am mapping my rna-seq reads using hisat2. My library is single-end strand-specific (dUTP) illumina-TrueSeq-Stranded.
I am confused about what option is correct. Hisat2 manual say:
"For single-end reads, use F or R. 'F' means a read corresponds to a transcript. 'R' means a read corresponds to the reverse complemented counterpart of a transcript"
is correct if I choose "F" option??. if I visualize my alignments in IGV for example, all my reads must be in "red color" ?
what means if i have blue and red?