bowtie2 options when mapping stranded single end reads I'm trying to map RNA-Seq reads generated using the NEB Ultra Directional kit is first strand reversed protocal. I'm using bowtie-2.3.5_1 to align against the mus musculuous (mm10) genome.  The reads are single ended.

It seems that --fr and --rf are relevant only for paired end options. I tried these options as well as not specifying either (default).

E.g.

$ bowtie2 --fr \
        --threads 20 \
        --very-sensitive \
        -x /reference/mus_musculus/mm10/ucsc_assmebly/illumina_download/Sequence/Bowtie2Index/genome \
        -U trimmed_out/my_trimmed.fq.gz \
        -S bowtie_fr_1.sam

$ samtools sort -n -o bowtie_fr_sort_1.sam bowtie_def_1.sam


I then compared the output of bowtie_rf_sort.sam bowtie_default_sort.sam and bowtie_fr_sort.sam.  They are basically identical excluding the header.

Question:

Does strandedness matter in this alignment? Perhaps I should care about the --nofw/--norc options? Am I missing something here?
I repeat what user172818 says...don't waste your time on bowtie or tophat.  Use STAR or HISAT2, or a pseudoaligner like kallisto with a transcriptome.