I have ~100 paired end mRNA seq data (150 Nt read size) that were sequenced by Illumina MiSeq. I have clipped the adapter by cutadapt. I am getting low mapping percentage. I used BWA, Bowtie2, and STAR. For STAR, I am getting 3-30% mapping. Bowtie2 ~40% and BWA 40-45%. I am using assembled transcriptome of my particular organism.
I thought probably I was messing up something with the adapter trimming. But for paired end, it should not be a big issue, I guess. What else could I messing up???