I have a transcriptomic data from a illumina single end, strand specific experiment, it is a meta transcriptomic sample. Actually I am analizing the transcripts of bacteria.
I am using bowtie2 to map the sequences to a reference genome, but they are strand-specific, and Bowtie2 does not have that option. That is why I want to use hisat2 in order to select the strand specific option.
As hisat2 considers splicing and bacterias do not have splicing. Do you recommend to use the option --no-spliced-alignment in order to do the aligment?